# Reading DEGs list exp1
# all model including subset data
DEG.objs.e1.v3.0annotation.all<-list.files(path=file.path("..","v3.0annotation","20170617-samples","output","FULLtoptag"),
pattern="(^leaf|^root)(\\.)(.+)(v3.0anno)(.csv)")
# read csv file (only full model)
DEG.count.list.e1.v3.0annotation.all<-lapply(DEG.objs.e1.v3.0annotation.all, function(x) read_csv(paste(file.path("..","v3.0annotation","20170617-samples","output","FULLtoptag"),"/",x,sep="")))
names(DEG.count.list.e1.v3.0annotation.all)<-gsub(".csv","",DEG.objs.e1.v3.0annotation.all)
DEG.count.list.e1.v3.0annotation.all[["root.R500.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05)
# A tibble: 383 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.26 4.60 33.9 5.82e-9 1.55e-4 AT1G… NLP4
2 2 BraA… 2.13 3.39 32.5 1.20e-8 1.60e-4 AT1G… <NA>
3 3 BraA… 2.23 1.67 31.4 2.05e-8 1.83e-4 AT3G… ABCA3
4 4 BraA… 1.70 3.81 30.6 3.14e-8 1.93e-4 AT3G… NF-YA6
5 5 BraA… -1.53 4.64 30.3 3.61e-8 1.93e-4 AT4G… <NA>
6 6 BraA… 1.28 3.98 29.2 6.42e-8 2.86e-4 AT5G… GLN1;4
7 7 BraA… -1.14 5.84 28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1
8 8 BraA… 0.988 5.18 28.2 1.09e-7 3.29e-4 AT5G… <NA>
9 9 BraA… 1.77 5.64 28.2 1.12e-7 3.29e-4 AT5G… ATDUR3
10 10 BraA… -1.37 3.74 27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1
# ... with 373 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
names(DEG.count.list.e1.v3.0annotation.all)
[1] "leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno"
[2] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[3] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[4] "leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"
[5] "leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"
[6] "leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
[7] "leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
[8] "leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"
[9] "leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"
[10] "leaf.R500.trtlive.DEGs.all.rD.v3.0anno"
[11] "leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"
[12] "leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"
[13] "leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"
[14] "leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"
[15] "leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"
[16] "leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno"
[17] "leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"
[18] "leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno"
[19] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"
[20] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"
[21] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[22] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[23] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"
[24] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"
[25] "leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
[26] "root.FPsc.trtlive.DEGs.all.rD.v3.0anno"
[27] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[28] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[29] "root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"
[30] "root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"
[31] "root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
[32] "root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
[33] "root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"
[34] "root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"
[35] "root.R500.trtlive.DEGs.all.rD.v3.0anno"
[36] "root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"
[37] "root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"
[38] "root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"
[39] "root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"
[40] "root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"
[41] "root.trt5E_live.DEGs.add.rB.rR500.v3.0anno"
[42] "root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"
[43] "root.trt5E_live.DEGs.add.rD.rR500.v3.0anno"
[44] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"
[45] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"
[46] "root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[47] "root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[48] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"
[49] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"
[50] "root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
# FDR<0.05
DEG.count.list.e1.v3.0annotation.all %>% map(filter(FDR<0.05)) # does not work
Error in filter(FDR < 0.05): object 'FDR' not found
DEG.count.list.e1.v3.0annotation.all.FDR0.05<-DEG.count.list.e1.v3.0annotation.all %>% map(function(df) filter(df,FDR<0.05)) # does work
names(DEG.count.list.e1.v3.0annotation.all.FDR0.05)
[1] "leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno"
[2] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[3] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[4] "leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"
[5] "leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"
[6] "leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
[7] "leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
[8] "leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"
[9] "leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"
[10] "leaf.R500.trtlive.DEGs.all.rD.v3.0anno"
[11] "leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"
[12] "leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"
[13] "leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"
[14] "leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"
[15] "leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"
[16] "leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno"
[17] "leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"
[18] "leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno"
[19] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"
[20] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"
[21] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[22] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[23] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"
[24] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"
[25] "leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
[26] "root.FPsc.trtlive.DEGs.all.rD.v3.0anno"
[27] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[28] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[29] "root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"
[30] "root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"
[31] "root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
[32] "root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
[33] "root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"
[34] "root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"
[35] "root.R500.trtlive.DEGs.all.rD.v3.0anno"
[36] "root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"
[37] "root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"
[38] "root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"
[39] "root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"
[40] "root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"
[41] "root.trt5E_live.DEGs.add.rB.rR500.v3.0anno"
[42] "root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"
[43] "root.trt5E_live.DEGs.add.rD.rR500.v3.0anno"
[44] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"
[45] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"
[46] "root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"
[47] "root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[48] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"
[49] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"
[50] "root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"
# playing with map and lapply
DEG.count.list.e1.v3.0annotation.all %>% map(~filter(.,FDR<0.05)) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 0.119 28.2 1.10e-7 0.00256 AT3G… <NA>
2 2 BraA… 2.44 0.460 24.1 9.03e-7 0.0105 AT1G… AtVTL1
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.1 1.28 1.76 6.28
2 2 BraA… -12.4 0.829 0.0153 6.99
3 3 BraA… 12.1 -0.791 1.16 6.40
4 4 BraA… -12.1 -0.0737 0.114 5.28
5 5 BraA… -12.1 -0.201 -0.825 6.50
6 6 BraA… -12.0 1.20 -0.163 5.28
7 7 BraA… -11.8 2.08 2.81 4.84
8 8 BraA… 11.7 -1.18 -0.702 6.97
9 9 BraA… -11.7 -0.149 -0.115 4.94
10 10 BraA… -11.6 0.0524 0.0330 4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.3 2.23 3.29 6.34
2 2 BraA… 12.8 -1.76 -1.60 5.99
3 3 BraA… -12.3 0.201 -0.624 6.50
4 4 BraA… -12.2 0.0737 0.188 5.28
5 5 BraA… 12.1 -1.17 -1.38 5.13
6 6 BraA… -11.9 1.27 1.98 5.04
7 7 BraA… -11.8 0.149 0.0341 4.94
8 8 BraA… -11.8 -1.28 0.481 6.28
9 9 BraA… -11.6 -0.0524 -0.0194 4.78
10 10 BraA… -11.5 -0.829 -0.814 6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… -12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… 12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… -12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… -11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… -11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… -11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… -11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… -11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… 11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… -12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… 12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… -12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… -11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… -11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… -11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… -11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… -11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… 11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.1 -1.28 -1.76 6.28
2 2 BraA… 12.4 -0.829 -0.0153 6.99
3 3 BraA… -12.1 0.791 -1.16 6.40
4 4 BraA… 12.1 0.0737 -0.114 5.28
5 5 BraA… 12.1 0.201 0.825 6.50
6 6 BraA… 12.0 -1.20 0.163 5.28
7 7 BraA… 11.8 -2.08 -2.81 4.84
8 8 BraA… -11.7 1.18 0.702 6.97
9 9 BraA… 11.7 0.149 0.115 4.94
10 10 BraA… 11.6 -0.0524 -0.0330 4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.3 -2.23 -3.29 6.34
2 2 BraA… -12.8 1.76 1.60 5.99
3 3 BraA… 12.3 -0.201 0.624 6.50
4 4 BraA… 12.2 -0.0737 -0.188 5.28
5 5 BraA… -12.1 1.17 1.38 5.13
6 6 BraA… 11.9 -1.27 -1.98 5.04
7 7 BraA… 11.8 -0.149 -0.0341 4.94
8 8 BraA… 11.8 1.28 -0.481 6.28
9 9 BraA… 11.6 0.0524 0.0194 4.78
10 10 BraA… 11.5 0.829 0.814 6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… 12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… -12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… 12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… 11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… 11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… 11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… 11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… 11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… -11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… 12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… -12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… 12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… 11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… 11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… 11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… 11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… 11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… -11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 1,927 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.06 5.13 64.4 9.98e-16 2.40e-11 AT2G… ATP5CS
2 2 BraA… -1.55 5.25 42.0 9.02e-11 1.09e- 6 AT5G… AtcPT4
3 3 BraA… -1.67 2.22 37.2 1.04e- 9 8.35e- 6 AT1G… ATGSTU25
4 4 BraA… -1.18 3.93 36.1 1.86e- 9 1.12e- 5 AT2G… ANNAT4
5 5 BraA… -2.08 1.98 35.7 2.33e- 9 1.12e- 5 AT5G… <NA>
6 6 BraA… 2.53 3.65 34.3 4.63e- 9 1.86e- 5 AT3G… CYP72A8
7 7 BraA… -1.63 1.89 33.7 6.36e- 9 2.19e- 5 AT5G… <NA>
8 8 BraA… -1.94 7.40 32.9 9.50e- 9 2.86e- 5 AT3G… UGP3
9 9 BraA… -2.93 2.43 32.6 1.10e- 8 2.95e- 5 AT1G… AtPFA-DS…
10 10 BraA… -2.27 6.82 32.4 1.24e- 8 2.99e- 5 AT1G… ATPPCK1
# ... with 1,917 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 2 x 12
X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.31 -1.19 4.33 30.4 2.49e-7
2 2 BraA… 5.60 -5.46 3.93 30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 2 x 12
X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.124 1.19 4.33 30.4 2.49e-7
2 2 BraA… 0.142 5.46 3.93 30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 144 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.617 3.31 29.9 4.54e-8 0.00114 AT1G… <NA>
2 2 BraA… -1.74 3.55 28.1 1.16e-7 0.00146 AT1G… AtWSCP
3 3 BraA… 0.579 3.07 24.4 7.75e-7 0.00619 AT5G… ATHIR1
4 4 BraA… -1.30 0.169 24.0 9.82e-7 0.00619 AT1G… GXM1
5 5 BraA… -0.573 5.72 22.0 2.77e-6 0.00936 AT1G… ADT1
6 6 BraA… -0.625 3.09 21.9 2.82e-6 0.00936 AT4G… GrxC5
7 7 BraA… -0.615 3.75 21.7 3.13e-6 0.00936 AT2G… ALF1
8 8 BraA… -1.63 2.99 21.7 3.26e-6 0.00936 AT1G… <NA>
9 9 BraA… 1.52 -0.158 21.6 3.34e-6 0.00936 AT4G… ATK5
10 10 BraA… -0.550 3.01 20.9 4.91e-6 0.0124 AT5G… <NA>
# ... with 134 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 144 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.617 3.31 29.9 4.54e-8 0.00114 AT1G… <NA>
2 2 BraA… -1.74 3.55 28.1 1.16e-7 0.00146 AT1G… AtWSCP
3 3 BraA… 0.579 3.07 24.4 7.75e-7 0.00619 AT5G… ATHIR1
4 4 BraA… -1.30 0.169 24.0 9.82e-7 0.00619 AT1G… GXM1
5 5 BraA… -0.573 5.72 22.0 2.77e-6 0.00936 AT1G… ADT1
6 6 BraA… -0.625 3.09 21.9 2.82e-6 0.00936 AT4G… GrxC5
7 7 BraA… -0.615 3.75 21.7 3.13e-6 0.00936 AT2G… ALF1
8 8 BraA… -1.63 2.99 21.7 3.26e-6 0.00936 AT1G… <NA>
9 9 BraA… 1.52 -0.158 21.6 3.34e-6 0.00936 AT4G… ATK5
10 10 BraA… -0.550 3.01 20.9 4.91e-6 0.0124 AT5G… <NA>
# ... with 134 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 1,932 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.63 1.26 38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25
2 2 BraA… -1.88 3.55 32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP
3 3 BraA… -0.737 3.75 31.1 2.45e- 8 1.44e-4 AT2G… ALF1
4 4 BraA… 1.25 0.725 31.0 2.56e- 8 1.44e-4 <NA> <NA>
5 5 BraA… 0.889 5.15 30.8 2.85e- 8 1.44e-4 AT5G… <NA>
6 6 BraA… 0.841 3.81 30.2 3.85e- 8 1.62e-4 AT5G… <NA>
7 7 BraA… 1.44 1.69 29.8 4.91e- 8 1.77e-4 AT1G… SMR2
8 8 BraA… 1.80 1.28 27.9 1.26e- 7 3.96e-4 AT3G… <NA>
9 9 BraA… 0.537 3.28 27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10 10 BraA… -0.370 5.90 26.9 2.18e- 7 5.36e-4 AT1G… ARC12
# ... with 1,922 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 1,932 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.63 1.26 38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25
2 2 BraA… -1.88 3.55 32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP
3 3 BraA… -0.737 3.75 31.1 2.45e- 8 1.44e-4 AT2G… ALF1
4 4 BraA… 1.25 0.725 31.0 2.56e- 8 1.44e-4 <NA> <NA>
5 5 BraA… 0.889 5.15 30.8 2.85e- 8 1.44e-4 AT5G… <NA>
6 6 BraA… 0.841 3.81 30.2 3.85e- 8 1.62e-4 AT5G… <NA>
7 7 BraA… 1.44 1.69 29.8 4.91e- 8 1.77e-4 AT1G… SMR2
8 8 BraA… 1.80 1.28 27.9 1.26e- 7 3.96e-4 AT3G… <NA>
9 9 BraA… 0.537 3.28 27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10 10 BraA… -0.370 5.90 26.9 2.18e- 7 5.36e-4 AT1G… ARC12
# ... with 1,922 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 399 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.44 1.44 3.15 45.2 1.53e-10
2 2 BraA… -0.107 4.00 1.98 37.2 8.22e- 9
3 3 BraA… 0.503 0.261 3.31 31.4 1.53e- 7
4 4 BraA… -5.55 4.85 6.89 30.8 2.02e- 7
5 5 BraA… -2.03 2.06 3.23 30.4 2.55e- 7
6 6 BraA… -0.842 0.719 7.36 29.9 3.24e- 7
7 7 BraA… -1.26 1.05 4.67 29.8 3.32e- 7
8 8 BraA… -1.73 1.82 2.32 29.7 3.54e- 7
9 9 BraA… 5.51 -5.39 3.93 29.1 4.72e- 7
10 10 BraA… -1.77 1.82 3.55 28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2,061 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.05 2.10 4.33 69.8 6.82e-16
2 2 BraA… -2.93 2.85 2.99 50.6 1.05e-11
3 3 BraA… 1.36 -1.10 4.25 45.3 1.44e-10
4 4 BraA… -2.25 1.85 7.95 44.9 1.77e-10
5 5 BraA… -1.06 0.665 3.75 44.7 1.94e-10
6 6 BraA… -2.43 1.96 3.99 42.5 5.87e-10
7 7 BraA… 2.36 -2.08 3.32 40.7 1.48e- 9
8 8 BraA… 1.22 -0.692 5.15 38.5 4.34e- 9
9 9 BraA… -1.67 1.09 1.26 38.2 4.98e- 9
10 10 BraA… -4.17 3.88 3.53 37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 5 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 4.00 1.98 34.5 4.19e-9 1.06e-4 <NA> <NA>
2 2 BraA… -5.39 3.93 21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3 3 BraA… 1.44 3.15 21.6 3.43e-6 2.89e-2 AT1G… ASB1
4 4 BraA… -4.43 2.62 20.2 7.13e-6 4.50e-2 AT2G… ATPEX10
5 5 BraA… 2.41 2.99 19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 8 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.10 4.33 35.4 2.65e-9 6.68e-5 AT2G… ATP5CS
2 2 BraA… 3.21 2.98 31.8 1.72e-8 2.17e-4 AT5G… ABCF2
3 3 BraA… 2.85 2.99 27.7 1.43e-7 1.20e-3 AT1G… AtPFA-DS…
4 4 BraA… 1.72 5.63 22.7 1.91e-6 1.20e-2 AT5G… AtcPT4
5 5 BraA… -3.46 2.58 21.0 4.51e-6 2.27e-2 AT1G… ATGPT2
6 6 BraA… 3.88 3.53 19.8 8.40e-6 3.53e-2 AT3G… ATACP5
7 7 BraA… -2.08 3.32 19.5 10.00e-6 3.60e-2 AT5G… <NA>
8 8 BraA… 2.81 1.29 19.0 1.31e-5 4.14e-2 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 399 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.00152 -1.44 3.15 45.2 1.53e-10
2 2 BraA… 3.89 -4.00 1.98 37.2 8.22e- 9
3 3 BraA… 0.764 -0.261 3.31 31.4 1.53e- 7
4 4 BraA… -0.695 -4.85 6.89 30.8 2.02e- 7
5 5 BraA… 0.0355 -2.06 3.23 30.4 2.55e- 7
6 6 BraA… -0.123 -0.719 7.36 29.9 3.24e- 7
7 7 BraA… -0.209 -1.05 4.67 29.8 3.32e- 7
8 8 BraA… 0.0889 -1.82 2.32 29.7 3.54e- 7
9 9 BraA… 0.117 5.39 3.93 29.1 4.72e- 7
10 10 BraA… 0.0435 -1.82 3.55 28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 2,061 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.0565 -2.10 4.33 69.8 6.82e-16
2 2 BraA… -0.0794 -2.85 2.99 50.6 1.05e-11
3 3 BraA… 0.263 1.10 4.25 45.3 1.44e-10
4 4 BraA… -0.407 -1.85 7.95 44.9 1.77e-10
5 5 BraA… -0.393 -0.665 3.75 44.7 1.94e-10
6 6 BraA… -0.471 -1.96 3.99 42.5 5.87e-10
7 7 BraA… 0.286 2.08 3.32 40.7 1.48e- 9
8 8 BraA… 0.523 0.692 5.15 38.5 4.34e- 9
9 9 BraA… -0.583 -1.09 1.26 38.2 4.98e- 9
10 10 BraA… -0.288 -3.88 3.53 37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 5 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -4.00 1.98 34.5 4.19e-9 1.06e-4 <NA> <NA>
2 2 BraA… 5.39 3.93 21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3 3 BraA… -1.44 3.15 21.6 3.43e-6 2.89e-2 AT1G… ASB1
4 4 BraA… 4.43 2.62 20.2 7.13e-6 4.50e-2 AT2G… ATPEX10
5 5 BraA… -2.41 2.99 19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 9 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.70 5.74 37.9 7.54e-10 1.99e-5 AT1G… <NA>
2 2 BraA… -2.70 0.746 27.1 1.92e- 7 2.53e-3 AT5G… CGLD27
3 3 BraA… 4.90 4.78 24.9 6.18e- 7 5.43e-3 AT5G… HSP18.2
4 4 BraA… 3.02 4.43 21.3 3.97e- 6 2.27e-2 AT5G… HSP18.2
5 5 BraA… -1.05 7.43 21.1 4.30e- 6 2.27e-2 AT1G… ATOPR2
6 6 BraA… -0.761 2.51 20.6 5.79e- 6 2.43e-2 AT1G… <NA>
7 7 BraA… 2.53 0.780 20.3 6.46e- 6 2.43e-2 AT3G… <NA>
8 8 BraA… -1.31 3.16 19.5 9.87e- 6 2.96e-2 AT3G… BHLH039
9 9 BraA… -0.938 6.99 19.5 1.01e- 5 2.96e-2 AT3G… AtDJ1A
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 14.4 -2.48 -2.08 7.57
2 2 BraA… -14.3 1.08 1.42 7.50
3 3 BraA… 13.6 -1.30 -0.0224 6.77
4 4 BraA… 13.0 -1.33 -1.99 6.18
5 5 BraA… -12.6 2.16 2.96 5.81
6 6 BraA… 12.5 -4.21 -4.13 5.83
7 7 BraA… 12.3 -0.131 -1.29 5.50
8 8 BraA… 12.3 -1.42 -0.269 5.36
9 9 BraA… 12.2 0.0831 -1.14 5.49
10 10 BraA… 12.1 -0.139 -2.13 5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.3 -1.28 0.0181 6.55
2 2 BraA… -13.2 -1.08 0.338 7.50
3 3 BraA… -13.2 1.76 1.23 6.43
4 4 BraA… -12.5 0.465 1.32 7.08
5 5 BraA… 12.3 -0.0831 -1.22 5.49
6 6 BraA… 12.2 1.30 1.28 6.77
7 7 BraA… 12.2 0.131 -1.16 5.50
8 8 BraA… -12.0 1.24 1.70 5.33
9 9 BraA… 12.0 0.139 -1.99 5.21
10 10 BraA… 11.9 2.48 0.395 7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… 13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… 12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… 12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… -12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… -11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… 11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… 11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… 11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… 11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… 13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… 12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… 12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… -12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… -11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… 11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… 11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… 11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… 11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -14.4 2.48 2.08 7.57
2 2 BraA… 14.3 -1.08 -1.42 7.50
3 3 BraA… -13.6 1.30 0.0224 6.77
4 4 BraA… -13.0 1.33 1.99 6.18
5 5 BraA… 12.6 -2.16 -2.96 5.81
6 6 BraA… -12.5 4.21 4.13 5.83
7 7 BraA… -12.3 0.131 1.29 5.50
8 8 BraA… -12.3 1.42 0.269 5.36
9 9 BraA… -12.2 -0.0831 1.14 5.49
10 10 BraA… -12.1 0.139 2.13 5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.3 1.28 -0.0181 6.55
2 2 BraA… 13.2 1.08 -0.338 7.50
3 3 BraA… 13.2 -1.76 -1.23 6.43
4 4 BraA… 12.5 -0.465 -1.32 7.08
5 5 BraA… -12.3 0.0831 1.22 5.49
6 6 BraA… -12.2 -1.30 -1.28 6.77
7 7 BraA… -12.2 -0.131 1.16 5.50
8 8 BraA… 12.0 -1.24 -1.70 5.33
9 9 BraA… -12.0 -0.139 1.99 5.21
10 10 BraA… -11.9 -2.48 -0.395 7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… -13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… -12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… -12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… 12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… 11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… -11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… -11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… -11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… -11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… -13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… -12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… -12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… 12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… 11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… -11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… -11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… -11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… -11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 383 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.26 4.60 33.9 5.82e-9 1.55e-4 AT1G… NLP4
2 2 BraA… 2.13 3.39 32.5 1.20e-8 1.60e-4 AT1G… <NA>
3 3 BraA… 2.23 1.67 31.4 2.05e-8 1.83e-4 AT3G… ABCA3
4 4 BraA… 1.70 3.81 30.6 3.14e-8 1.93e-4 AT3G… NF-YA6
5 5 BraA… -1.53 4.64 30.3 3.61e-8 1.93e-4 AT4G… <NA>
6 6 BraA… 1.28 3.98 29.2 6.42e-8 2.86e-4 AT5G… GLN1;4
7 7 BraA… -1.14 5.84 28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1
8 8 BraA… 0.988 5.18 28.2 1.09e-7 3.29e-4 AT5G… <NA>
9 9 BraA… 1.77 5.64 28.2 1.12e-7 3.29e-4 AT5G… ATDUR3
10 10 BraA… -1.37 3.74 27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1
# ... with 373 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 23 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.42 2.28 32.0 1.53e-8 4.27e-4 AT5G… <NA>
2 2 BraA… 1.99 1.62 26.6 2.46e-7 3.43e-3 AT4G… CYP82C4
3 3 BraA… 0.941 2.67 24.2 8.86e-7 7.05e-3 AT3G… <NA>
4 4 BraA… 1.81 1.53 23.9 1.01e-6 7.05e-3 AT4G… ATIRT1
5 5 BraA… 1.67 0.0566 20.8 5.15e-6 2.73e-2 AT1G… <NA>
6 6 BraA… 1.43 0.469 20.5 5.87e-6 2.73e-2 AT2G… Iqd4
7 7 BraA… 1.42 2.16 19.9 8.24e-6 3.28e-2 AT2G… <NA>
8 8 BraA… 1.45 3.39 19.5 1.02e-5 3.28e-2 AT5G… <NA>
9 9 BraA… 1.47 2.36 19.2 1.16e-5 3.28e-2 AT5G… ATPT4
10 10 BraA… -4.78 -0.507 19.1 1.26e-5 3.28e-2 <NA> <NA>
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 23 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.42 2.28 32.0 1.53e-8 4.27e-4 AT5G… <NA>
2 2 BraA… 1.99 1.62 26.6 2.46e-7 3.43e-3 AT4G… CYP82C4
3 3 BraA… 0.941 2.67 24.2 8.86e-7 7.05e-3 AT3G… <NA>
4 4 BraA… 1.81 1.53 23.9 1.01e-6 7.05e-3 AT4G… ATIRT1
5 5 BraA… 1.67 0.0566 20.8 5.15e-6 2.73e-2 AT1G… <NA>
6 6 BraA… 1.43 0.469 20.5 5.87e-6 2.73e-2 AT2G… Iqd4
7 7 BraA… 1.42 2.16 19.9 8.24e-6 3.28e-2 AT2G… <NA>
8 8 BraA… 1.45 3.39 19.5 1.02e-5 3.28e-2 AT5G… <NA>
9 9 BraA… 1.47 2.36 19.2 1.16e-5 3.28e-2 AT5G… ATPT4
10 10 BraA… -4.78 -0.507 19.1 1.26e-5 3.28e-2 <NA> <NA>
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 40 x 12
X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.0755 2.15 6.68 39.4 2.73e-9
2 2 BraA… 0.797 1.55 1.62 37.3 8.04e-9
3 3 BraA… 1.41 0.0163 2.28 30.9 1.99e-7
4 4 BraA… 0.882 1.65 1.59 28.4 6.96e-7
5 5 BraA… 0.770 1.39 3.39 27.0 1.38e-6
6 6 BraA… -0.174 1.33 2.87 26.4 1.82e-6
7 7 BraA… -0.0525 -3.86 2.45 26.3 1.93e-6
8 8 BraA… 0.143 2.27 2.81 24.9 3.94e-6
9 9 BraA… 0.901 1.15 0.469 24.2 5.61e-6
10 10 BraA… 0.0770 1.36 9.03 23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 40 x 12
X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.07 -2.15 6.68 39.4 2.73e-9
2 2 BraA… 2.35 -1.55 1.62 37.3 8.04e-9
3 3 BraA… 1.42 -0.0163 2.28 30.9 1.99e-7
4 4 BraA… 2.53 -1.65 1.59 28.4 6.96e-7
5 5 BraA… 2.16 -1.39 3.39 27.0 1.38e-6
6 6 BraA… 1.16 -1.33 2.87 26.4 1.82e-6
7 7 BraA… -3.92 3.86 2.45 26.3 1.93e-6
8 8 BraA… 2.41 -2.27 2.81 24.9 3.94e-6
9 9 BraA… 2.06 -1.15 0.469 24.2 5.61e-6
10 10 BraA… 1.44 -1.36 9.03 23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 931 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.28 2.79 48.3 3.58e-12 9.97e-8 AT2G… <NA>
2 2 BraA… -0.853 7.44 39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A
3 3 BraA… -1.01 5.65 38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1
4 4 BraA… -0.728 6.87 36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A
5 5 BraA… 1.11 3.16 33.4 7.41e- 9 4.13e-5 AT4G… AAT1
6 6 BraA… 2.09 1.69 32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8
7 7 BraA… 1.41 0.714 30.2 3.96e- 8 1.58e-4 AT1G… <NA>
8 8 BraA… 1.30 2.16 29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19
9 9 BraA… 1.12 1.66 28.4 9.71e- 8 2.49e-4 AT4G… <NA>
10 10 BraA… 1.23 3.30 28.3 1.02e- 7 2.49e-4 AT3G… LAC7
# ... with 921 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 931 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.28 2.79 48.3 3.58e-12 9.97e-8 AT2G… <NA>
2 2 BraA… -0.853 7.44 39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A
3 3 BraA… -1.01 5.65 38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1
4 4 BraA… -0.728 6.87 36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A
5 5 BraA… 1.11 3.16 33.4 7.41e- 9 4.13e-5 AT4G… AAT1
6 6 BraA… 2.09 1.69 32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8
7 7 BraA… 1.41 0.714 30.2 3.96e- 8 1.58e-4 AT1G… <NA>
8 8 BraA… 1.30 2.16 29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19
9 9 BraA… 1.12 1.66 28.4 9.71e- 8 2.49e-4 AT4G… <NA>
10 10 BraA… 1.23 3.30 28.3 1.02e- 7 2.49e-4 AT3G… LAC7
# ... with 921 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 26 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.37 2.49 35.6 2.39e-9 6.66e-5 AT3G… BHLH039
2 2 BraA… -1.38 1.82 31.6 1.93e-8 2.20e-4 AT3G… BHLH039
3 3 BraA… -0.754 7.44 31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A
4 4 BraA… -0.648 6.87 28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A
5 5 BraA… -0.600 5.31 27.9 1.30e-7 7.24e-4 AT4G… UGT73B1
6 6 BraA… -0.616 5.60 27.0 2.02e-7 9.37e-4 AT4G… UGT73B1
7 7 BraA… 1.21 2.58 26.2 3.10e-7 1.04e-3 AT1G… TAR4
8 8 BraA… -0.831 5.65 26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1
9 9 BraA… 1.69 3.06 26.0 3.37e-7 1.04e-3 AT1G… <NA>
10 10 BraA… -1.10 7.15 24.8 6.25e-7 1.74e-3 AT1G… <NA>
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 26 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.37 2.49 35.6 2.39e-9 6.66e-5 AT3G… BHLH039
2 2 BraA… -1.38 1.82 31.6 1.93e-8 2.20e-4 AT3G… BHLH039
3 3 BraA… -0.754 7.44 31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A
4 4 BraA… -0.648 6.87 28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A
5 5 BraA… -0.600 5.31 27.9 1.30e-7 7.24e-4 AT4G… UGT73B1
6 6 BraA… -0.616 5.60 27.0 2.02e-7 9.37e-4 AT4G… UGT73B1
7 7 BraA… 1.21 2.58 26.2 3.10e-7 1.04e-3 AT1G… TAR4
8 8 BraA… -0.831 5.65 26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1
9 9 BraA… 1.69 3.06 26.0 3.37e-7 1.04e-3 AT1G… <NA>
10 10 BraA… -1.10 7.15 24.8 6.25e-7 1.74e-3 AT1G… <NA>
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 608 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.45 0.859 5.65 53.8 2.04e-12
2 2 BraA… -1.55 0.526 2.79 53.2 2.87e-12
3 3 BraA… -0.697 -1.05 7.15 44.3 2.45e-10
4 4 BraA… -0.663 -0.389 7.44 42.9 4.75e-10
5 5 BraA… -0.556 -0.349 6.87 38.8 3.76e- 9
6 6 BraA… 1.06 1.83 1.59 38.6 4.18e- 9
7 7 BraA… 1.73 -0.931 2.16 38.6 4.25e- 9
8 8 BraA… 0.900 0.654 3.16 37.9 5.79e- 9
9 9 BraA… 0.946 1.34 5.01 36.4 1.23e- 8
10 10 BraA… 0.527 0.753 4.69 35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 77 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.538 -1.21 7.15 41.7 8.66e-10
2 2 BraA… -1.14 0.590 5.65 35.9 1.59e- 8
3 3 BraA… -1.50 0.191 2.49 35.1 2.43e- 8
4 4 BraA… -0.581 -0.358 7.44 33.9 4.30e- 8
5 5 BraA… 2.22 -2.33 1.23 33.7 4.91e- 8
6 6 BraA… 1.57 -1.36 4.01 31.8 1.26e- 7
7 7 BraA… -0.836 -1.91 0.848 31.7 1.32e- 7
8 8 BraA… -1.58 0.333 1.82 31.2 1.66e- 7
9 9 BraA… -0.529 -0.246 6.87 30.4 2.55e- 7
10 10 BraA… 1.69 -1.46 3.49 29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 4 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -4.86 4.91 25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2 2 BraA… 3.42 0.428 25.7 3.93e-7 0.00548 AT5G… <NA>
3 3 BraA… -1.55 1.93 20.4 6.29e-6 0.0453 AT4G… UBC17
4 4 BraA… 2.02 6.68 20.3 6.50e-6 0.0453 AT4G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 3.28 1.39 23.8 1.05e-6 0.0293 AT3G… <NA>
2 2 BraA… 2.95 0.428 21.5 3.55e-6 0.0495 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 608 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.590 -0.859 5.65 53.8 2.04e-12
2 2 BraA… -1.03 -0.526 2.79 53.2 2.87e-12
3 3 BraA… -1.74 1.05 7.15 44.3 2.45e-10
4 4 BraA… -1.05 0.389 7.44 42.9 4.75e-10
5 5 BraA… -0.905 0.349 6.87 38.8 3.76e- 9
6 6 BraA… 2.89 -1.83 1.59 38.6 4.18e- 9
7 7 BraA… 0.799 0.931 2.16 38.6 4.25e- 9
8 8 BraA… 1.55 -0.654 3.16 37.9 5.79e- 9
9 9 BraA… 2.29 -1.34 5.01 36.4 1.23e- 8
10 10 BraA… 1.28 -0.753 4.69 35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 77 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.75 1.21 7.15 41.7 8.66e-10
2 2 BraA… -0.554 -0.590 5.65 35.9 1.59e- 8
3 3 BraA… -1.31 -0.191 2.49 35.1 2.43e- 8
4 4 BraA… -0.939 0.358 7.44 33.9 4.30e- 8
5 5 BraA… -0.113 2.33 1.23 33.7 4.91e- 8
6 6 BraA… 0.211 1.36 4.01 31.8 1.26e- 7
7 7 BraA… -2.75 1.91 0.848 31.7 1.32e- 7
8 8 BraA… -1.25 -0.333 1.82 31.2 1.66e- 7
9 9 BraA… -0.775 0.246 6.87 30.4 2.55e- 7
10 10 BraA… 0.236 1.46 3.49 29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 4 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 4.86 4.91 25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2 2 BraA… -3.42 0.428 25.7 3.93e-7 0.00548 AT5G… <NA>
3 3 BraA… 1.55 1.93 20.4 6.29e-6 0.0453 AT4G… UBC17
4 4 BraA… -2.02 6.68 20.3 6.50e-6 0.0453 AT4G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
DEG.count.list.e1.v3.0annotation.all %>% map(nrow) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
[1] 23327
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 25210
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 25210
$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
[1] 25210
$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
[1] 25210
$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210
$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
[1] 25210
$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
[1] 25210
$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
[1] 25210
$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
[1] 24087
$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
[1] 25210
$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
[1] 25210
$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
[1] 25210
$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210
$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
[1] 25210
$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
[1] 25210
$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
[1] 25210
$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
[1] 25210
$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210
$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
[1] 26380
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 27887
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 27887
$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
[1] 27887
$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
[1] 27887
$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887
$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
[1] 27887
$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
[1] 27887
$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
[1] 27887
$root.R500.trtlive.DEGs.all.rD.v3.0anno
[1] 26690
$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
[1] 27887
$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
[1] 27887
$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
[1] 27887
$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887
$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
[1] 27887
$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
[1] 27887
$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
[1] 27887
$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
[1] 27887
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
[1] 27887
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
[1] 27887
$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 27887
$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 27887
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
[1] 27887
$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887
map(DEG.count.list.e1.v3.0annotation.all,~filter(.x,FDR<0.05)) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 0.119 28.2 1.10e-7 0.00256 AT3G… <NA>
2 2 BraA… 2.44 0.460 24.1 9.03e-7 0.0105 AT1G… AtVTL1
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.1 1.28 1.76 6.28
2 2 BraA… -12.4 0.829 0.0153 6.99
3 3 BraA… 12.1 -0.791 1.16 6.40
4 4 BraA… -12.1 -0.0737 0.114 5.28
5 5 BraA… -12.1 -0.201 -0.825 6.50
6 6 BraA… -12.0 1.20 -0.163 5.28
7 7 BraA… -11.8 2.08 2.81 4.84
8 8 BraA… 11.7 -1.18 -0.702 6.97
9 9 BraA… -11.7 -0.149 -0.115 4.94
10 10 BraA… -11.6 0.0524 0.0330 4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.3 2.23 3.29 6.34
2 2 BraA… 12.8 -1.76 -1.60 5.99
3 3 BraA… -12.3 0.201 -0.624 6.50
4 4 BraA… -12.2 0.0737 0.188 5.28
5 5 BraA… 12.1 -1.17 -1.38 5.13
6 6 BraA… -11.9 1.27 1.98 5.04
7 7 BraA… -11.8 0.149 0.0341 4.94
8 8 BraA… -11.8 -1.28 0.481 6.28
9 9 BraA… -11.6 -0.0524 -0.0194 4.78
10 10 BraA… -11.5 -0.829 -0.814 6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… -12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… 12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… -12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… -11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… -11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… -11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… -11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… -11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… 11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… -12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… 12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… -12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… -11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… -11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… -11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… -11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… -11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… 11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.1 -1.28 -1.76 6.28
2 2 BraA… 12.4 -0.829 -0.0153 6.99
3 3 BraA… -12.1 0.791 -1.16 6.40
4 4 BraA… 12.1 0.0737 -0.114 5.28
5 5 BraA… 12.1 0.201 0.825 6.50
6 6 BraA… 12.0 -1.20 0.163 5.28
7 7 BraA… 11.8 -2.08 -2.81 4.84
8 8 BraA… -11.7 1.18 0.702 6.97
9 9 BraA… 11.7 0.149 0.115 4.94
10 10 BraA… 11.6 -0.0524 -0.0330 4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.3 -2.23 -3.29 6.34
2 2 BraA… -12.8 1.76 1.60 5.99
3 3 BraA… 12.3 -0.201 0.624 6.50
4 4 BraA… 12.2 -0.0737 -0.188 5.28
5 5 BraA… -12.1 1.17 1.38 5.13
6 6 BraA… 11.9 -1.27 -1.98 5.04
7 7 BraA… 11.8 -0.149 -0.0341 4.94
8 8 BraA… 11.8 1.28 -0.481 6.28
9 9 BraA… 11.6 0.0524 0.0194 4.78
10 10 BraA… 11.5 0.829 0.814 6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… 12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… -12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… 12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… 11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… 11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… 11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… 11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… 11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… -11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… 12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… -12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… 12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… 11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… 11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… 11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… 11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… 11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… -11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 1,927 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.06 5.13 64.4 9.98e-16 2.40e-11 AT2G… ATP5CS
2 2 BraA… -1.55 5.25 42.0 9.02e-11 1.09e- 6 AT5G… AtcPT4
3 3 BraA… -1.67 2.22 37.2 1.04e- 9 8.35e- 6 AT1G… ATGSTU25
4 4 BraA… -1.18 3.93 36.1 1.86e- 9 1.12e- 5 AT2G… ANNAT4
5 5 BraA… -2.08 1.98 35.7 2.33e- 9 1.12e- 5 AT5G… <NA>
6 6 BraA… 2.53 3.65 34.3 4.63e- 9 1.86e- 5 AT3G… CYP72A8
7 7 BraA… -1.63 1.89 33.7 6.36e- 9 2.19e- 5 AT5G… <NA>
8 8 BraA… -1.94 7.40 32.9 9.50e- 9 2.86e- 5 AT3G… UGP3
9 9 BraA… -2.93 2.43 32.6 1.10e- 8 2.95e- 5 AT1G… AtPFA-DS…
10 10 BraA… -2.27 6.82 32.4 1.24e- 8 2.99e- 5 AT1G… ATPPCK1
# ... with 1,917 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 2 x 12
X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.31 -1.19 4.33 30.4 2.49e-7
2 2 BraA… 5.60 -5.46 3.93 30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 2 x 12
X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.124 1.19 4.33 30.4 2.49e-7
2 2 BraA… 0.142 5.46 3.93 30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 144 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.617 3.31 29.9 4.54e-8 0.00114 AT1G… <NA>
2 2 BraA… -1.74 3.55 28.1 1.16e-7 0.00146 AT1G… AtWSCP
3 3 BraA… 0.579 3.07 24.4 7.75e-7 0.00619 AT5G… ATHIR1
4 4 BraA… -1.30 0.169 24.0 9.82e-7 0.00619 AT1G… GXM1
5 5 BraA… -0.573 5.72 22.0 2.77e-6 0.00936 AT1G… ADT1
6 6 BraA… -0.625 3.09 21.9 2.82e-6 0.00936 AT4G… GrxC5
7 7 BraA… -0.615 3.75 21.7 3.13e-6 0.00936 AT2G… ALF1
8 8 BraA… -1.63 2.99 21.7 3.26e-6 0.00936 AT1G… <NA>
9 9 BraA… 1.52 -0.158 21.6 3.34e-6 0.00936 AT4G… ATK5
10 10 BraA… -0.550 3.01 20.9 4.91e-6 0.0124 AT5G… <NA>
# ... with 134 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 144 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.617 3.31 29.9 4.54e-8 0.00114 AT1G… <NA>
2 2 BraA… -1.74 3.55 28.1 1.16e-7 0.00146 AT1G… AtWSCP
3 3 BraA… 0.579 3.07 24.4 7.75e-7 0.00619 AT5G… ATHIR1
4 4 BraA… -1.30 0.169 24.0 9.82e-7 0.00619 AT1G… GXM1
5 5 BraA… -0.573 5.72 22.0 2.77e-6 0.00936 AT1G… ADT1
6 6 BraA… -0.625 3.09 21.9 2.82e-6 0.00936 AT4G… GrxC5
7 7 BraA… -0.615 3.75 21.7 3.13e-6 0.00936 AT2G… ALF1
8 8 BraA… -1.63 2.99 21.7 3.26e-6 0.00936 AT1G… <NA>
9 9 BraA… 1.52 -0.158 21.6 3.34e-6 0.00936 AT4G… ATK5
10 10 BraA… -0.550 3.01 20.9 4.91e-6 0.0124 AT5G… <NA>
# ... with 134 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 1,932 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.63 1.26 38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25
2 2 BraA… -1.88 3.55 32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP
3 3 BraA… -0.737 3.75 31.1 2.45e- 8 1.44e-4 AT2G… ALF1
4 4 BraA… 1.25 0.725 31.0 2.56e- 8 1.44e-4 <NA> <NA>
5 5 BraA… 0.889 5.15 30.8 2.85e- 8 1.44e-4 AT5G… <NA>
6 6 BraA… 0.841 3.81 30.2 3.85e- 8 1.62e-4 AT5G… <NA>
7 7 BraA… 1.44 1.69 29.8 4.91e- 8 1.77e-4 AT1G… SMR2
8 8 BraA… 1.80 1.28 27.9 1.26e- 7 3.96e-4 AT3G… <NA>
9 9 BraA… 0.537 3.28 27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10 10 BraA… -0.370 5.90 26.9 2.18e- 7 5.36e-4 AT1G… ARC12
# ... with 1,922 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 1,932 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.63 1.26 38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25
2 2 BraA… -1.88 3.55 32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP
3 3 BraA… -0.737 3.75 31.1 2.45e- 8 1.44e-4 AT2G… ALF1
4 4 BraA… 1.25 0.725 31.0 2.56e- 8 1.44e-4 <NA> <NA>
5 5 BraA… 0.889 5.15 30.8 2.85e- 8 1.44e-4 AT5G… <NA>
6 6 BraA… 0.841 3.81 30.2 3.85e- 8 1.62e-4 AT5G… <NA>
7 7 BraA… 1.44 1.69 29.8 4.91e- 8 1.77e-4 AT1G… SMR2
8 8 BraA… 1.80 1.28 27.9 1.26e- 7 3.96e-4 AT3G… <NA>
9 9 BraA… 0.537 3.28 27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10 10 BraA… -0.370 5.90 26.9 2.18e- 7 5.36e-4 AT1G… ARC12
# ... with 1,922 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 399 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.44 1.44 3.15 45.2 1.53e-10
2 2 BraA… -0.107 4.00 1.98 37.2 8.22e- 9
3 3 BraA… 0.503 0.261 3.31 31.4 1.53e- 7
4 4 BraA… -5.55 4.85 6.89 30.8 2.02e- 7
5 5 BraA… -2.03 2.06 3.23 30.4 2.55e- 7
6 6 BraA… -0.842 0.719 7.36 29.9 3.24e- 7
7 7 BraA… -1.26 1.05 4.67 29.8 3.32e- 7
8 8 BraA… -1.73 1.82 2.32 29.7 3.54e- 7
9 9 BraA… 5.51 -5.39 3.93 29.1 4.72e- 7
10 10 BraA… -1.77 1.82 3.55 28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2,061 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.05 2.10 4.33 69.8 6.82e-16
2 2 BraA… -2.93 2.85 2.99 50.6 1.05e-11
3 3 BraA… 1.36 -1.10 4.25 45.3 1.44e-10
4 4 BraA… -2.25 1.85 7.95 44.9 1.77e-10
5 5 BraA… -1.06 0.665 3.75 44.7 1.94e-10
6 6 BraA… -2.43 1.96 3.99 42.5 5.87e-10
7 7 BraA… 2.36 -2.08 3.32 40.7 1.48e- 9
8 8 BraA… 1.22 -0.692 5.15 38.5 4.34e- 9
9 9 BraA… -1.67 1.09 1.26 38.2 4.98e- 9
10 10 BraA… -4.17 3.88 3.53 37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 5 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 4.00 1.98 34.5 4.19e-9 1.06e-4 <NA> <NA>
2 2 BraA… -5.39 3.93 21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3 3 BraA… 1.44 3.15 21.6 3.43e-6 2.89e-2 AT1G… ASB1
4 4 BraA… -4.43 2.62 20.2 7.13e-6 4.50e-2 AT2G… ATPEX10
5 5 BraA… 2.41 2.99 19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 8 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.10 4.33 35.4 2.65e-9 6.68e-5 AT2G… ATP5CS
2 2 BraA… 3.21 2.98 31.8 1.72e-8 2.17e-4 AT5G… ABCF2
3 3 BraA… 2.85 2.99 27.7 1.43e-7 1.20e-3 AT1G… AtPFA-DS…
4 4 BraA… 1.72 5.63 22.7 1.91e-6 1.20e-2 AT5G… AtcPT4
5 5 BraA… -3.46 2.58 21.0 4.51e-6 2.27e-2 AT1G… ATGPT2
6 6 BraA… 3.88 3.53 19.8 8.40e-6 3.53e-2 AT3G… ATACP5
7 7 BraA… -2.08 3.32 19.5 10.00e-6 3.60e-2 AT5G… <NA>
8 8 BraA… 2.81 1.29 19.0 1.31e-5 4.14e-2 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 399 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.00152 -1.44 3.15 45.2 1.53e-10
2 2 BraA… 3.89 -4.00 1.98 37.2 8.22e- 9
3 3 BraA… 0.764 -0.261 3.31 31.4 1.53e- 7
4 4 BraA… -0.695 -4.85 6.89 30.8 2.02e- 7
5 5 BraA… 0.0355 -2.06 3.23 30.4 2.55e- 7
6 6 BraA… -0.123 -0.719 7.36 29.9 3.24e- 7
7 7 BraA… -0.209 -1.05 4.67 29.8 3.32e- 7
8 8 BraA… 0.0889 -1.82 2.32 29.7 3.54e- 7
9 9 BraA… 0.117 5.39 3.93 29.1 4.72e- 7
10 10 BraA… 0.0435 -1.82 3.55 28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 2,061 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.0565 -2.10 4.33 69.8 6.82e-16
2 2 BraA… -0.0794 -2.85 2.99 50.6 1.05e-11
3 3 BraA… 0.263 1.10 4.25 45.3 1.44e-10
4 4 BraA… -0.407 -1.85 7.95 44.9 1.77e-10
5 5 BraA… -0.393 -0.665 3.75 44.7 1.94e-10
6 6 BraA… -0.471 -1.96 3.99 42.5 5.87e-10
7 7 BraA… 0.286 2.08 3.32 40.7 1.48e- 9
8 8 BraA… 0.523 0.692 5.15 38.5 4.34e- 9
9 9 BraA… -0.583 -1.09 1.26 38.2 4.98e- 9
10 10 BraA… -0.288 -3.88 3.53 37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 5 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -4.00 1.98 34.5 4.19e-9 1.06e-4 <NA> <NA>
2 2 BraA… 5.39 3.93 21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3 3 BraA… -1.44 3.15 21.6 3.43e-6 2.89e-2 AT1G… ASB1
4 4 BraA… 4.43 2.62 20.2 7.13e-6 4.50e-2 AT2G… ATPEX10
5 5 BraA… -2.41 2.99 19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 9 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.70 5.74 37.9 7.54e-10 1.99e-5 AT1G… <NA>
2 2 BraA… -2.70 0.746 27.1 1.92e- 7 2.53e-3 AT5G… CGLD27
3 3 BraA… 4.90 4.78 24.9 6.18e- 7 5.43e-3 AT5G… HSP18.2
4 4 BraA… 3.02 4.43 21.3 3.97e- 6 2.27e-2 AT5G… HSP18.2
5 5 BraA… -1.05 7.43 21.1 4.30e- 6 2.27e-2 AT1G… ATOPR2
6 6 BraA… -0.761 2.51 20.6 5.79e- 6 2.43e-2 AT1G… <NA>
7 7 BraA… 2.53 0.780 20.3 6.46e- 6 2.43e-2 AT3G… <NA>
8 8 BraA… -1.31 3.16 19.5 9.87e- 6 2.96e-2 AT3G… BHLH039
9 9 BraA… -0.938 6.99 19.5 1.01e- 5 2.96e-2 AT3G… AtDJ1A
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 14.4 -2.48 -2.08 7.57
2 2 BraA… -14.3 1.08 1.42 7.50
3 3 BraA… 13.6 -1.30 -0.0224 6.77
4 4 BraA… 13.0 -1.33 -1.99 6.18
5 5 BraA… -12.6 2.16 2.96 5.81
6 6 BraA… 12.5 -4.21 -4.13 5.83
7 7 BraA… 12.3 -0.131 -1.29 5.50
8 8 BraA… 12.3 -1.42 -0.269 5.36
9 9 BraA… 12.2 0.0831 -1.14 5.49
10 10 BraA… 12.1 -0.139 -2.13 5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.3 -1.28 0.0181 6.55
2 2 BraA… -13.2 -1.08 0.338 7.50
3 3 BraA… -13.2 1.76 1.23 6.43
4 4 BraA… -12.5 0.465 1.32 7.08
5 5 BraA… 12.3 -0.0831 -1.22 5.49
6 6 BraA… 12.2 1.30 1.28 6.77
7 7 BraA… 12.2 0.131 -1.16 5.50
8 8 BraA… -12.0 1.24 1.70 5.33
9 9 BraA… 12.0 0.139 -1.99 5.21
10 10 BraA… 11.9 2.48 0.395 7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… 13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… 12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… 12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… -12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… -11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… 11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… 11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… 11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… 11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… 13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… 12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… 12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… -12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… -11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… 11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… 11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… 11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… 11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -14.4 2.48 2.08 7.57
2 2 BraA… 14.3 -1.08 -1.42 7.50
3 3 BraA… -13.6 1.30 0.0224 6.77
4 4 BraA… -13.0 1.33 1.99 6.18
5 5 BraA… 12.6 -2.16 -2.96 5.81
6 6 BraA… -12.5 4.21 4.13 5.83
7 7 BraA… -12.3 0.131 1.29 5.50
8 8 BraA… -12.3 1.42 0.269 5.36
9 9 BraA… -12.2 -0.0831 1.14 5.49
10 10 BraA… -12.1 0.139 2.13 5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.3 1.28 -0.0181 6.55
2 2 BraA… 13.2 1.08 -0.338 7.50
3 3 BraA… 13.2 -1.76 -1.23 6.43
4 4 BraA… 12.5 -0.465 -1.32 7.08
5 5 BraA… -12.3 0.0831 1.22 5.49
6 6 BraA… -12.2 -1.30 -1.28 6.77
7 7 BraA… -12.2 -0.131 1.16 5.50
8 8 BraA… 12.0 -1.24 -1.70 5.33
9 9 BraA… -12.0 -0.139 1.99 5.21
10 10 BraA… -11.9 -2.48 -0.395 7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… -13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… -12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… -12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… 12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… 11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… -11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… -11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… -11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… -11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… -13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… -12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… -12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… 12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… 11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… -11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… -11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… -11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… -11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 383 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.26 4.60 33.9 5.82e-9 1.55e-4 AT1G… NLP4
2 2 BraA… 2.13 3.39 32.5 1.20e-8 1.60e-4 AT1G… <NA>
3 3 BraA… 2.23 1.67 31.4 2.05e-8 1.83e-4 AT3G… ABCA3
4 4 BraA… 1.70 3.81 30.6 3.14e-8 1.93e-4 AT3G… NF-YA6
5 5 BraA… -1.53 4.64 30.3 3.61e-8 1.93e-4 AT4G… <NA>
6 6 BraA… 1.28 3.98 29.2 6.42e-8 2.86e-4 AT5G… GLN1;4
7 7 BraA… -1.14 5.84 28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1
8 8 BraA… 0.988 5.18 28.2 1.09e-7 3.29e-4 AT5G… <NA>
9 9 BraA… 1.77 5.64 28.2 1.12e-7 3.29e-4 AT5G… ATDUR3
10 10 BraA… -1.37 3.74 27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1
# ... with 373 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 23 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.42 2.28 32.0 1.53e-8 4.27e-4 AT5G… <NA>
2 2 BraA… 1.99 1.62 26.6 2.46e-7 3.43e-3 AT4G… CYP82C4
3 3 BraA… 0.941 2.67 24.2 8.86e-7 7.05e-3 AT3G… <NA>
4 4 BraA… 1.81 1.53 23.9 1.01e-6 7.05e-3 AT4G… ATIRT1
5 5 BraA… 1.67 0.0566 20.8 5.15e-6 2.73e-2 AT1G… <NA>
6 6 BraA… 1.43 0.469 20.5 5.87e-6 2.73e-2 AT2G… Iqd4
7 7 BraA… 1.42 2.16 19.9 8.24e-6 3.28e-2 AT2G… <NA>
8 8 BraA… 1.45 3.39 19.5 1.02e-5 3.28e-2 AT5G… <NA>
9 9 BraA… 1.47 2.36 19.2 1.16e-5 3.28e-2 AT5G… ATPT4
10 10 BraA… -4.78 -0.507 19.1 1.26e-5 3.28e-2 <NA> <NA>
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 23 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.42 2.28 32.0 1.53e-8 4.27e-4 AT5G… <NA>
2 2 BraA… 1.99 1.62 26.6 2.46e-7 3.43e-3 AT4G… CYP82C4
3 3 BraA… 0.941 2.67 24.2 8.86e-7 7.05e-3 AT3G… <NA>
4 4 BraA… 1.81 1.53 23.9 1.01e-6 7.05e-3 AT4G… ATIRT1
5 5 BraA… 1.67 0.0566 20.8 5.15e-6 2.73e-2 AT1G… <NA>
6 6 BraA… 1.43 0.469 20.5 5.87e-6 2.73e-2 AT2G… Iqd4
7 7 BraA… 1.42 2.16 19.9 8.24e-6 3.28e-2 AT2G… <NA>
8 8 BraA… 1.45 3.39 19.5 1.02e-5 3.28e-2 AT5G… <NA>
9 9 BraA… 1.47 2.36 19.2 1.16e-5 3.28e-2 AT5G… ATPT4
10 10 BraA… -4.78 -0.507 19.1 1.26e-5 3.28e-2 <NA> <NA>
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 40 x 12
X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.0755 2.15 6.68 39.4 2.73e-9
2 2 BraA… 0.797 1.55 1.62 37.3 8.04e-9
3 3 BraA… 1.41 0.0163 2.28 30.9 1.99e-7
4 4 BraA… 0.882 1.65 1.59 28.4 6.96e-7
5 5 BraA… 0.770 1.39 3.39 27.0 1.38e-6
6 6 BraA… -0.174 1.33 2.87 26.4 1.82e-6
7 7 BraA… -0.0525 -3.86 2.45 26.3 1.93e-6
8 8 BraA… 0.143 2.27 2.81 24.9 3.94e-6
9 9 BraA… 0.901 1.15 0.469 24.2 5.61e-6
10 10 BraA… 0.0770 1.36 9.03 23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 40 x 12
X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.07 -2.15 6.68 39.4 2.73e-9
2 2 BraA… 2.35 -1.55 1.62 37.3 8.04e-9
3 3 BraA… 1.42 -0.0163 2.28 30.9 1.99e-7
4 4 BraA… 2.53 -1.65 1.59 28.4 6.96e-7
5 5 BraA… 2.16 -1.39 3.39 27.0 1.38e-6
6 6 BraA… 1.16 -1.33 2.87 26.4 1.82e-6
7 7 BraA… -3.92 3.86 2.45 26.3 1.93e-6
8 8 BraA… 2.41 -2.27 2.81 24.9 3.94e-6
9 9 BraA… 2.06 -1.15 0.469 24.2 5.61e-6
10 10 BraA… 1.44 -1.36 9.03 23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 931 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.28 2.79 48.3 3.58e-12 9.97e-8 AT2G… <NA>
2 2 BraA… -0.853 7.44 39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A
3 3 BraA… -1.01 5.65 38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1
4 4 BraA… -0.728 6.87 36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A
5 5 BraA… 1.11 3.16 33.4 7.41e- 9 4.13e-5 AT4G… AAT1
6 6 BraA… 2.09 1.69 32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8
7 7 BraA… 1.41 0.714 30.2 3.96e- 8 1.58e-4 AT1G… <NA>
8 8 BraA… 1.30 2.16 29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19
9 9 BraA… 1.12 1.66 28.4 9.71e- 8 2.49e-4 AT4G… <NA>
10 10 BraA… 1.23 3.30 28.3 1.02e- 7 2.49e-4 AT3G… LAC7
# ... with 921 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 931 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.28 2.79 48.3 3.58e-12 9.97e-8 AT2G… <NA>
2 2 BraA… -0.853 7.44 39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A
3 3 BraA… -1.01 5.65 38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1
4 4 BraA… -0.728 6.87 36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A
5 5 BraA… 1.11 3.16 33.4 7.41e- 9 4.13e-5 AT4G… AAT1
6 6 BraA… 2.09 1.69 32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8
7 7 BraA… 1.41 0.714 30.2 3.96e- 8 1.58e-4 AT1G… <NA>
8 8 BraA… 1.30 2.16 29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19
9 9 BraA… 1.12 1.66 28.4 9.71e- 8 2.49e-4 AT4G… <NA>
10 10 BraA… 1.23 3.30 28.3 1.02e- 7 2.49e-4 AT3G… LAC7
# ... with 921 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 26 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.37 2.49 35.6 2.39e-9 6.66e-5 AT3G… BHLH039
2 2 BraA… -1.38 1.82 31.6 1.93e-8 2.20e-4 AT3G… BHLH039
3 3 BraA… -0.754 7.44 31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A
4 4 BraA… -0.648 6.87 28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A
5 5 BraA… -0.600 5.31 27.9 1.30e-7 7.24e-4 AT4G… UGT73B1
6 6 BraA… -0.616 5.60 27.0 2.02e-7 9.37e-4 AT4G… UGT73B1
7 7 BraA… 1.21 2.58 26.2 3.10e-7 1.04e-3 AT1G… TAR4
8 8 BraA… -0.831 5.65 26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1
9 9 BraA… 1.69 3.06 26.0 3.37e-7 1.04e-3 AT1G… <NA>
10 10 BraA… -1.10 7.15 24.8 6.25e-7 1.74e-3 AT1G… <NA>
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 26 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.37 2.49 35.6 2.39e-9 6.66e-5 AT3G… BHLH039
2 2 BraA… -1.38 1.82 31.6 1.93e-8 2.20e-4 AT3G… BHLH039
3 3 BraA… -0.754 7.44 31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A
4 4 BraA… -0.648 6.87 28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A
5 5 BraA… -0.600 5.31 27.9 1.30e-7 7.24e-4 AT4G… UGT73B1
6 6 BraA… -0.616 5.60 27.0 2.02e-7 9.37e-4 AT4G… UGT73B1
7 7 BraA… 1.21 2.58 26.2 3.10e-7 1.04e-3 AT1G… TAR4
8 8 BraA… -0.831 5.65 26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1
9 9 BraA… 1.69 3.06 26.0 3.37e-7 1.04e-3 AT1G… <NA>
10 10 BraA… -1.10 7.15 24.8 6.25e-7 1.74e-3 AT1G… <NA>
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 608 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.45 0.859 5.65 53.8 2.04e-12
2 2 BraA… -1.55 0.526 2.79 53.2 2.87e-12
3 3 BraA… -0.697 -1.05 7.15 44.3 2.45e-10
4 4 BraA… -0.663 -0.389 7.44 42.9 4.75e-10
5 5 BraA… -0.556 -0.349 6.87 38.8 3.76e- 9
6 6 BraA… 1.06 1.83 1.59 38.6 4.18e- 9
7 7 BraA… 1.73 -0.931 2.16 38.6 4.25e- 9
8 8 BraA… 0.900 0.654 3.16 37.9 5.79e- 9
9 9 BraA… 0.946 1.34 5.01 36.4 1.23e- 8
10 10 BraA… 0.527 0.753 4.69 35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 77 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.538 -1.21 7.15 41.7 8.66e-10
2 2 BraA… -1.14 0.590 5.65 35.9 1.59e- 8
3 3 BraA… -1.50 0.191 2.49 35.1 2.43e- 8
4 4 BraA… -0.581 -0.358 7.44 33.9 4.30e- 8
5 5 BraA… 2.22 -2.33 1.23 33.7 4.91e- 8
6 6 BraA… 1.57 -1.36 4.01 31.8 1.26e- 7
7 7 BraA… -0.836 -1.91 0.848 31.7 1.32e- 7
8 8 BraA… -1.58 0.333 1.82 31.2 1.66e- 7
9 9 BraA… -0.529 -0.246 6.87 30.4 2.55e- 7
10 10 BraA… 1.69 -1.46 3.49 29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 4 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -4.86 4.91 25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2 2 BraA… 3.42 0.428 25.7 3.93e-7 0.00548 AT5G… <NA>
3 3 BraA… -1.55 1.93 20.4 6.29e-6 0.0453 AT4G… UBC17
4 4 BraA… 2.02 6.68 20.3 6.50e-6 0.0453 AT4G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 3.28 1.39 23.8 1.05e-6 0.0293 AT3G… <NA>
2 2 BraA… 2.95 0.428 21.5 3.55e-6 0.0495 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 608 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.590 -0.859 5.65 53.8 2.04e-12
2 2 BraA… -1.03 -0.526 2.79 53.2 2.87e-12
3 3 BraA… -1.74 1.05 7.15 44.3 2.45e-10
4 4 BraA… -1.05 0.389 7.44 42.9 4.75e-10
5 5 BraA… -0.905 0.349 6.87 38.8 3.76e- 9
6 6 BraA… 2.89 -1.83 1.59 38.6 4.18e- 9
7 7 BraA… 0.799 0.931 2.16 38.6 4.25e- 9
8 8 BraA… 1.55 -0.654 3.16 37.9 5.79e- 9
9 9 BraA… 2.29 -1.34 5.01 36.4 1.23e- 8
10 10 BraA… 1.28 -0.753 4.69 35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 77 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.75 1.21 7.15 41.7 8.66e-10
2 2 BraA… -0.554 -0.590 5.65 35.9 1.59e- 8
3 3 BraA… -1.31 -0.191 2.49 35.1 2.43e- 8
4 4 BraA… -0.939 0.358 7.44 33.9 4.30e- 8
5 5 BraA… -0.113 2.33 1.23 33.7 4.91e- 8
6 6 BraA… 0.211 1.36 4.01 31.8 1.26e- 7
7 7 BraA… -2.75 1.91 0.848 31.7 1.32e- 7
8 8 BraA… -1.25 -0.333 1.82 31.2 1.66e- 7
9 9 BraA… -0.775 0.246 6.87 30.4 2.55e- 7
10 10 BraA… 0.236 1.46 3.49 29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 4 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 4.86 4.91 25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2 2 BraA… -3.42 0.428 25.7 3.93e-7 0.00548 AT5G… <NA>
3 3 BraA… 1.55 1.93 20.4 6.29e-6 0.0453 AT4G… UBC17
4 4 BraA… -2.02 6.68 20.3 6.50e-6 0.0453 AT4G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
lapply(DEG.count.list.e1.v3.0annotation.all,function(df) filter(df,FDR<0.05)) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 0.119 28.2 1.10e-7 0.00256 AT3G… <NA>
2 2 BraA… 2.44 0.460 24.1 9.03e-7 0.0105 AT1G… AtVTL1
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.1 1.28 1.76 6.28
2 2 BraA… -12.4 0.829 0.0153 6.99
3 3 BraA… 12.1 -0.791 1.16 6.40
4 4 BraA… -12.1 -0.0737 0.114 5.28
5 5 BraA… -12.1 -0.201 -0.825 6.50
6 6 BraA… -12.0 1.20 -0.163 5.28
7 7 BraA… -11.8 2.08 2.81 4.84
8 8 BraA… 11.7 -1.18 -0.702 6.97
9 9 BraA… -11.7 -0.149 -0.115 4.94
10 10 BraA… -11.6 0.0524 0.0330 4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.3 2.23 3.29 6.34
2 2 BraA… 12.8 -1.76 -1.60 5.99
3 3 BraA… -12.3 0.201 -0.624 6.50
4 4 BraA… -12.2 0.0737 0.188 5.28
5 5 BraA… 12.1 -1.17 -1.38 5.13
6 6 BraA… -11.9 1.27 1.98 5.04
7 7 BraA… -11.8 0.149 0.0341 4.94
8 8 BraA… -11.8 -1.28 0.481 6.28
9 9 BraA… -11.6 -0.0524 -0.0194 4.78
10 10 BraA… -11.5 -0.829 -0.814 6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… -12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… 12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… -12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… -11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… -11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… -11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… -11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… -11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… 11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… -12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… 12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… -12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… -11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… -11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… -11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… -11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… -11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… 11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.1 -1.28 -1.76 6.28
2 2 BraA… 12.4 -0.829 -0.0153 6.99
3 3 BraA… -12.1 0.791 -1.16 6.40
4 4 BraA… 12.1 0.0737 -0.114 5.28
5 5 BraA… 12.1 0.201 0.825 6.50
6 6 BraA… 12.0 -1.20 0.163 5.28
7 7 BraA… 11.8 -2.08 -2.81 4.84
8 8 BraA… -11.7 1.18 0.702 6.97
9 9 BraA… 11.7 0.149 0.115 4.94
10 10 BraA… 11.6 -0.0524 -0.0330 4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 18,895 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.3 -2.23 -3.29 6.34
2 2 BraA… -12.8 1.76 1.60 5.99
3 3 BraA… 12.3 -0.201 0.624 6.50
4 4 BraA… 12.2 -0.0737 -0.188 5.28
5 5 BraA… -12.1 1.17 1.38 5.13
6 6 BraA… 11.9 -1.27 -1.98 5.04
7 7 BraA… 11.8 -0.149 -0.0341 4.94
8 8 BraA… 11.8 1.28 -0.481 6.28
9 9 BraA… 11.6 0.0524 0.0194 4.78
10 10 BraA… 11.5 0.829 0.814 6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… 12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… -12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… 12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… 11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… 11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… 11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… 11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… 11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… -11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 19,658 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 12.4 6.50 2505. 0 0 AT1G… TAR4
2 2 BraA… 12.1 5.28 4344. 0 0 <NA> <NA>
3 3 BraA… -12.1 6.40 3411. 0 0 AT2G… ATCNGC11
4 4 BraA… 12.1 6.99 1955. 0 0 AT4G… CRK39
5 5 BraA… 11.9 6.28 1578. 0 0 AT1G… ATBBD1
6 6 BraA… 11.8 4.94 1986. 0 0 <NA> <NA>
7 7 BraA… 11.6 4.78 3000. 0 0 <NA> <NA>
8 8 BraA… 11.6 5.28 3458. 0 0 AT1G… <NA>
9 9 BraA… 11.5 4.63 2430. 0 0 AT5G… <NA>
10 10 BraA… -11.4 5.99 5024. 0 0 <NA> <NA>
# ... with 19,648 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 1,927 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.06 5.13 64.4 9.98e-16 2.40e-11 AT2G… ATP5CS
2 2 BraA… -1.55 5.25 42.0 9.02e-11 1.09e- 6 AT5G… AtcPT4
3 3 BraA… -1.67 2.22 37.2 1.04e- 9 8.35e- 6 AT1G… ATGSTU25
4 4 BraA… -1.18 3.93 36.1 1.86e- 9 1.12e- 5 AT2G… ANNAT4
5 5 BraA… -2.08 1.98 35.7 2.33e- 9 1.12e- 5 AT5G… <NA>
6 6 BraA… 2.53 3.65 34.3 4.63e- 9 1.86e- 5 AT3G… CYP72A8
7 7 BraA… -1.63 1.89 33.7 6.36e- 9 2.19e- 5 AT5G… <NA>
8 8 BraA… -1.94 7.40 32.9 9.50e- 9 2.86e- 5 AT3G… UGP3
9 9 BraA… -2.93 2.43 32.6 1.10e- 8 2.95e- 5 AT1G… AtPFA-DS…
10 10 BraA… -2.27 6.82 32.4 1.24e- 8 2.99e- 5 AT1G… ATPPCK1
# ... with 1,917 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 2 x 12
X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.31 -1.19 4.33 30.4 2.49e-7
2 2 BraA… 5.60 -5.46 3.93 30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 2 x 12
X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.124 1.19 4.33 30.4 2.49e-7
2 2 BraA… 0.142 5.46 3.93 30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 144 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.617 3.31 29.9 4.54e-8 0.00114 AT1G… <NA>
2 2 BraA… -1.74 3.55 28.1 1.16e-7 0.00146 AT1G… AtWSCP
3 3 BraA… 0.579 3.07 24.4 7.75e-7 0.00619 AT5G… ATHIR1
4 4 BraA… -1.30 0.169 24.0 9.82e-7 0.00619 AT1G… GXM1
5 5 BraA… -0.573 5.72 22.0 2.77e-6 0.00936 AT1G… ADT1
6 6 BraA… -0.625 3.09 21.9 2.82e-6 0.00936 AT4G… GrxC5
7 7 BraA… -0.615 3.75 21.7 3.13e-6 0.00936 AT2G… ALF1
8 8 BraA… -1.63 2.99 21.7 3.26e-6 0.00936 AT1G… <NA>
9 9 BraA… 1.52 -0.158 21.6 3.34e-6 0.00936 AT4G… ATK5
10 10 BraA… -0.550 3.01 20.9 4.91e-6 0.0124 AT5G… <NA>
# ... with 134 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 144 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.617 3.31 29.9 4.54e-8 0.00114 AT1G… <NA>
2 2 BraA… -1.74 3.55 28.1 1.16e-7 0.00146 AT1G… AtWSCP
3 3 BraA… 0.579 3.07 24.4 7.75e-7 0.00619 AT5G… ATHIR1
4 4 BraA… -1.30 0.169 24.0 9.82e-7 0.00619 AT1G… GXM1
5 5 BraA… -0.573 5.72 22.0 2.77e-6 0.00936 AT1G… ADT1
6 6 BraA… -0.625 3.09 21.9 2.82e-6 0.00936 AT4G… GrxC5
7 7 BraA… -0.615 3.75 21.7 3.13e-6 0.00936 AT2G… ALF1
8 8 BraA… -1.63 2.99 21.7 3.26e-6 0.00936 AT1G… <NA>
9 9 BraA… 1.52 -0.158 21.6 3.34e-6 0.00936 AT4G… ATK5
10 10 BraA… -0.550 3.01 20.9 4.91e-6 0.0124 AT5G… <NA>
# ... with 134 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 1,932 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.63 1.26 38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25
2 2 BraA… -1.88 3.55 32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP
3 3 BraA… -0.737 3.75 31.1 2.45e- 8 1.44e-4 AT2G… ALF1
4 4 BraA… 1.25 0.725 31.0 2.56e- 8 1.44e-4 <NA> <NA>
5 5 BraA… 0.889 5.15 30.8 2.85e- 8 1.44e-4 AT5G… <NA>
6 6 BraA… 0.841 3.81 30.2 3.85e- 8 1.62e-4 AT5G… <NA>
7 7 BraA… 1.44 1.69 29.8 4.91e- 8 1.77e-4 AT1G… SMR2
8 8 BraA… 1.80 1.28 27.9 1.26e- 7 3.96e-4 AT3G… <NA>
9 9 BraA… 0.537 3.28 27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10 10 BraA… -0.370 5.90 26.9 2.18e- 7 5.36e-4 AT1G… ARC12
# ... with 1,922 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 1,932 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.63 1.26 38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25
2 2 BraA… -1.88 3.55 32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP
3 3 BraA… -0.737 3.75 31.1 2.45e- 8 1.44e-4 AT2G… ALF1
4 4 BraA… 1.25 0.725 31.0 2.56e- 8 1.44e-4 <NA> <NA>
5 5 BraA… 0.889 5.15 30.8 2.85e- 8 1.44e-4 AT5G… <NA>
6 6 BraA… 0.841 3.81 30.2 3.85e- 8 1.62e-4 AT5G… <NA>
7 7 BraA… 1.44 1.69 29.8 4.91e- 8 1.77e-4 AT1G… SMR2
8 8 BraA… 1.80 1.28 27.9 1.26e- 7 3.96e-4 AT3G… <NA>
9 9 BraA… 0.537 3.28 27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10 10 BraA… -0.370 5.90 26.9 2.18e- 7 5.36e-4 AT1G… ARC12
# ... with 1,922 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 399 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.44 1.44 3.15 45.2 1.53e-10
2 2 BraA… -0.107 4.00 1.98 37.2 8.22e- 9
3 3 BraA… 0.503 0.261 3.31 31.4 1.53e- 7
4 4 BraA… -5.55 4.85 6.89 30.8 2.02e- 7
5 5 BraA… -2.03 2.06 3.23 30.4 2.55e- 7
6 6 BraA… -0.842 0.719 7.36 29.9 3.24e- 7
7 7 BraA… -1.26 1.05 4.67 29.8 3.32e- 7
8 8 BraA… -1.73 1.82 2.32 29.7 3.54e- 7
9 9 BraA… 5.51 -5.39 3.93 29.1 4.72e- 7
10 10 BraA… -1.77 1.82 3.55 28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2,061 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.05 2.10 4.33 69.8 6.82e-16
2 2 BraA… -2.93 2.85 2.99 50.6 1.05e-11
3 3 BraA… 1.36 -1.10 4.25 45.3 1.44e-10
4 4 BraA… -2.25 1.85 7.95 44.9 1.77e-10
5 5 BraA… -1.06 0.665 3.75 44.7 1.94e-10
6 6 BraA… -2.43 1.96 3.99 42.5 5.87e-10
7 7 BraA… 2.36 -2.08 3.32 40.7 1.48e- 9
8 8 BraA… 1.22 -0.692 5.15 38.5 4.34e- 9
9 9 BraA… -1.67 1.09 1.26 38.2 4.98e- 9
10 10 BraA… -4.17 3.88 3.53 37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 5 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 4.00 1.98 34.5 4.19e-9 1.06e-4 <NA> <NA>
2 2 BraA… -5.39 3.93 21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3 3 BraA… 1.44 3.15 21.6 3.43e-6 2.89e-2 AT1G… ASB1
4 4 BraA… -4.43 2.62 20.2 7.13e-6 4.50e-2 AT2G… ATPEX10
5 5 BraA… 2.41 2.99 19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 8 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.10 4.33 35.4 2.65e-9 6.68e-5 AT2G… ATP5CS
2 2 BraA… 3.21 2.98 31.8 1.72e-8 2.17e-4 AT5G… ABCF2
3 3 BraA… 2.85 2.99 27.7 1.43e-7 1.20e-3 AT1G… AtPFA-DS…
4 4 BraA… 1.72 5.63 22.7 1.91e-6 1.20e-2 AT5G… AtcPT4
5 5 BraA… -3.46 2.58 21.0 4.51e-6 2.27e-2 AT1G… ATGPT2
6 6 BraA… 3.88 3.53 19.8 8.40e-6 3.53e-2 AT3G… ATACP5
7 7 BraA… -2.08 3.32 19.5 10.00e-6 3.60e-2 AT5G… <NA>
8 8 BraA… 2.81 1.29 19.0 1.31e-5 4.14e-2 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 399 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.00152 -1.44 3.15 45.2 1.53e-10
2 2 BraA… 3.89 -4.00 1.98 37.2 8.22e- 9
3 3 BraA… 0.764 -0.261 3.31 31.4 1.53e- 7
4 4 BraA… -0.695 -4.85 6.89 30.8 2.02e- 7
5 5 BraA… 0.0355 -2.06 3.23 30.4 2.55e- 7
6 6 BraA… -0.123 -0.719 7.36 29.9 3.24e- 7
7 7 BraA… -0.209 -1.05 4.67 29.8 3.32e- 7
8 8 BraA… 0.0889 -1.82 2.32 29.7 3.54e- 7
9 9 BraA… 0.117 5.39 3.93 29.1 4.72e- 7
10 10 BraA… 0.0435 -1.82 3.55 28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 2,061 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.0565 -2.10 4.33 69.8 6.82e-16
2 2 BraA… -0.0794 -2.85 2.99 50.6 1.05e-11
3 3 BraA… 0.263 1.10 4.25 45.3 1.44e-10
4 4 BraA… -0.407 -1.85 7.95 44.9 1.77e-10
5 5 BraA… -0.393 -0.665 3.75 44.7 1.94e-10
6 6 BraA… -0.471 -1.96 3.99 42.5 5.87e-10
7 7 BraA… 0.286 2.08 3.32 40.7 1.48e- 9
8 8 BraA… 0.523 0.692 5.15 38.5 4.34e- 9
9 9 BraA… -0.583 -1.09 1.26 38.2 4.98e- 9
10 10 BraA… -0.288 -3.88 3.53 37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 5 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -4.00 1.98 34.5 4.19e-9 1.06e-4 <NA> <NA>
2 2 BraA… 5.39 3.93 21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3 3 BraA… -1.44 3.15 21.6 3.43e-6 2.89e-2 AT1G… ASB1
4 4 BraA… 4.43 2.62 20.2 7.13e-6 4.50e-2 AT2G… ATPEX10
5 5 BraA… -2.41 2.99 19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 9 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.70 5.74 37.9 7.54e-10 1.99e-5 AT1G… <NA>
2 2 BraA… -2.70 0.746 27.1 1.92e- 7 2.53e-3 AT5G… CGLD27
3 3 BraA… 4.90 4.78 24.9 6.18e- 7 5.43e-3 AT5G… HSP18.2
4 4 BraA… 3.02 4.43 21.3 3.97e- 6 2.27e-2 AT5G… HSP18.2
5 5 BraA… -1.05 7.43 21.1 4.30e- 6 2.27e-2 AT1G… ATOPR2
6 6 BraA… -0.761 2.51 20.6 5.79e- 6 2.43e-2 AT1G… <NA>
7 7 BraA… 2.53 0.780 20.3 6.46e- 6 2.43e-2 AT3G… <NA>
8 8 BraA… -1.31 3.16 19.5 9.87e- 6 2.96e-2 AT3G… BHLH039
9 9 BraA… -0.938 6.99 19.5 1.01e- 5 2.96e-2 AT3G… AtDJ1A
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 14.4 -2.48 -2.08 7.57
2 2 BraA… -14.3 1.08 1.42 7.50
3 3 BraA… 13.6 -1.30 -0.0224 6.77
4 4 BraA… 13.0 -1.33 -1.99 6.18
5 5 BraA… -12.6 2.16 2.96 5.81
6 6 BraA… 12.5 -4.21 -4.13 5.83
7 7 BraA… 12.3 -0.131 -1.29 5.50
8 8 BraA… 12.3 -1.42 -0.269 5.36
9 9 BraA… 12.2 0.0831 -1.14 5.49
10 10 BraA… 12.1 -0.139 -2.13 5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 13.3 -1.28 0.0181 6.55
2 2 BraA… -13.2 -1.08 0.338 7.50
3 3 BraA… -13.2 1.76 1.23 6.43
4 4 BraA… -12.5 0.465 1.32 7.08
5 5 BraA… 12.3 -0.0831 -1.22 5.49
6 6 BraA… 12.2 1.30 1.28 6.77
7 7 BraA… 12.2 0.131 -1.16 5.50
8 8 BraA… -12.0 1.24 1.70 5.33
9 9 BraA… 12.0 0.139 -1.99 5.21
10 10 BraA… 11.9 2.48 0.395 7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… 13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… 12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… 12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… -12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… -11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… 11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… 11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… 11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… 11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… 13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… 12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… 12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… -12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… -11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… 11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… 11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… 11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… 11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -14.4 2.48 2.08 7.57
2 2 BraA… 14.3 -1.08 -1.42 7.50
3 3 BraA… -13.6 1.30 0.0224 6.77
4 4 BraA… -13.0 1.33 1.99 6.18
5 5 BraA… 12.6 -2.16 -2.96 5.81
6 6 BraA… -12.5 4.21 4.13 5.83
7 7 BraA… -12.3 0.131 1.29 5.50
8 8 BraA… -12.3 1.42 0.269 5.36
9 9 BraA… -12.2 -0.0831 1.14 5.49
10 10 BraA… -12.1 0.139 2.13 5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 17,373 x 13
X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
<int> <chr> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -13.3 1.28 -0.0181 6.55
2 2 BraA… 13.2 1.08 -0.338 7.50
3 3 BraA… 13.2 -1.76 -1.23 6.43
4 4 BraA… 12.5 -0.465 -1.32 7.08
5 5 BraA… -12.3 0.0831 1.22 5.49
6 6 BraA… -12.2 -1.30 -1.28 6.77
7 7 BraA… -12.2 -0.131 1.16 5.50
8 8 BraA… 12.0 -1.24 -1.70 5.33
9 9 BraA… -12.0 -0.139 1.99 5.21
10 10 BraA… -11.9 -2.48 -0.395 7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
# FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
# perc_ID <dbl>
$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… -13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… -12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… -12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… 12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… 11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… -11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… -11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… -11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… -11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 18,989 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 13.4 7.50 3038. 0 0 AT1G… <NA>
2 2 BraA… -13.0 6.77 1714. 0 0 <NA> <NA>
3 3 BraA… -12.8 6.55 5105. 0 0 <NA> <NA>
4 4 BraA… -12.6 7.57 2909. 0 0 AT2G… <NA>
5 5 BraA… 12.0 6.43 5449. 0 0 <NA> <NA>
6 6 BraA… 11.8 7.08 3622. 0 0 AT3G… <NA>
7 7 BraA… -11.7 5.50 3920. 0 0 <NA> <NA>
8 8 BraA… -11.7 5.49 3480. 0 0 <NA> <NA>
9 9 BraA… -11.7 6.18 3861. 0 0 AT5G… <NA>
10 10 BraA… -11.6 5.36 2391. 0 0 <NA> <NA>
# ... with 18,979 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 383 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.26 4.60 33.9 5.82e-9 1.55e-4 AT1G… NLP4
2 2 BraA… 2.13 3.39 32.5 1.20e-8 1.60e-4 AT1G… <NA>
3 3 BraA… 2.23 1.67 31.4 2.05e-8 1.83e-4 AT3G… ABCA3
4 4 BraA… 1.70 3.81 30.6 3.14e-8 1.93e-4 AT3G… NF-YA6
5 5 BraA… -1.53 4.64 30.3 3.61e-8 1.93e-4 AT4G… <NA>
6 6 BraA… 1.28 3.98 29.2 6.42e-8 2.86e-4 AT5G… GLN1;4
7 7 BraA… -1.14 5.84 28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1
8 8 BraA… 0.988 5.18 28.2 1.09e-7 3.29e-4 AT5G… <NA>
9 9 BraA… 1.77 5.64 28.2 1.12e-7 3.29e-4 AT5G… ATDUR3
10 10 BraA… -1.37 3.74 27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1
# ... with 373 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 23 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.42 2.28 32.0 1.53e-8 4.27e-4 AT5G… <NA>
2 2 BraA… 1.99 1.62 26.6 2.46e-7 3.43e-3 AT4G… CYP82C4
3 3 BraA… 0.941 2.67 24.2 8.86e-7 7.05e-3 AT3G… <NA>
4 4 BraA… 1.81 1.53 23.9 1.01e-6 7.05e-3 AT4G… ATIRT1
5 5 BraA… 1.67 0.0566 20.8 5.15e-6 2.73e-2 AT1G… <NA>
6 6 BraA… 1.43 0.469 20.5 5.87e-6 2.73e-2 AT2G… Iqd4
7 7 BraA… 1.42 2.16 19.9 8.24e-6 3.28e-2 AT2G… <NA>
8 8 BraA… 1.45 3.39 19.5 1.02e-5 3.28e-2 AT5G… <NA>
9 9 BraA… 1.47 2.36 19.2 1.16e-5 3.28e-2 AT5G… ATPT4
10 10 BraA… -4.78 -0.507 19.1 1.26e-5 3.28e-2 <NA> <NA>
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 23 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.42 2.28 32.0 1.53e-8 4.27e-4 AT5G… <NA>
2 2 BraA… 1.99 1.62 26.6 2.46e-7 3.43e-3 AT4G… CYP82C4
3 3 BraA… 0.941 2.67 24.2 8.86e-7 7.05e-3 AT3G… <NA>
4 4 BraA… 1.81 1.53 23.9 1.01e-6 7.05e-3 AT4G… ATIRT1
5 5 BraA… 1.67 0.0566 20.8 5.15e-6 2.73e-2 AT1G… <NA>
6 6 BraA… 1.43 0.469 20.5 5.87e-6 2.73e-2 AT2G… Iqd4
7 7 BraA… 1.42 2.16 19.9 8.24e-6 3.28e-2 AT2G… <NA>
8 8 BraA… 1.45 3.39 19.5 1.02e-5 3.28e-2 AT5G… <NA>
9 9 BraA… 1.47 2.36 19.2 1.16e-5 3.28e-2 AT5G… ATPT4
10 10 BraA… -4.78 -0.507 19.1 1.26e-5 3.28e-2 <NA> <NA>
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 40 x 12
X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.0755 2.15 6.68 39.4 2.73e-9
2 2 BraA… 0.797 1.55 1.62 37.3 8.04e-9
3 3 BraA… 1.41 0.0163 2.28 30.9 1.99e-7
4 4 BraA… 0.882 1.65 1.59 28.4 6.96e-7
5 5 BraA… 0.770 1.39 3.39 27.0 1.38e-6
6 6 BraA… -0.174 1.33 2.87 26.4 1.82e-6
7 7 BraA… -0.0525 -3.86 2.45 26.3 1.93e-6
8 8 BraA… 0.143 2.27 2.81 24.9 3.94e-6
9 9 BraA… 0.901 1.15 0.469 24.2 5.61e-6
10 10 BraA… 0.0770 1.36 9.03 23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 40 x 12
X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.07 -2.15 6.68 39.4 2.73e-9
2 2 BraA… 2.35 -1.55 1.62 37.3 8.04e-9
3 3 BraA… 1.42 -0.0163 2.28 30.9 1.99e-7
4 4 BraA… 2.53 -1.65 1.59 28.4 6.96e-7
5 5 BraA… 2.16 -1.39 3.39 27.0 1.38e-6
6 6 BraA… 1.16 -1.33 2.87 26.4 1.82e-6
7 7 BraA… -3.92 3.86 2.45 26.3 1.93e-6
8 8 BraA… 2.41 -2.27 2.81 24.9 3.94e-6
9 9 BraA… 2.06 -1.15 0.469 24.2 5.61e-6
10 10 BraA… 1.44 -1.36 9.03 23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 931 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.28 2.79 48.3 3.58e-12 9.97e-8 AT2G… <NA>
2 2 BraA… -0.853 7.44 39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A
3 3 BraA… -1.01 5.65 38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1
4 4 BraA… -0.728 6.87 36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A
5 5 BraA… 1.11 3.16 33.4 7.41e- 9 4.13e-5 AT4G… AAT1
6 6 BraA… 2.09 1.69 32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8
7 7 BraA… 1.41 0.714 30.2 3.96e- 8 1.58e-4 AT1G… <NA>
8 8 BraA… 1.30 2.16 29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19
9 9 BraA… 1.12 1.66 28.4 9.71e- 8 2.49e-4 AT4G… <NA>
10 10 BraA… 1.23 3.30 28.3 1.02e- 7 2.49e-4 AT3G… LAC7
# ... with 921 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 931 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.28 2.79 48.3 3.58e-12 9.97e-8 AT2G… <NA>
2 2 BraA… -0.853 7.44 39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A
3 3 BraA… -1.01 5.65 38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1
4 4 BraA… -0.728 6.87 36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A
5 5 BraA… 1.11 3.16 33.4 7.41e- 9 4.13e-5 AT4G… AAT1
6 6 BraA… 2.09 1.69 32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8
7 7 BraA… 1.41 0.714 30.2 3.96e- 8 1.58e-4 AT1G… <NA>
8 8 BraA… 1.30 2.16 29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19
9 9 BraA… 1.12 1.66 28.4 9.71e- 8 2.49e-4 AT4G… <NA>
10 10 BraA… 1.23 3.30 28.3 1.02e- 7 2.49e-4 AT3G… LAC7
# ... with 921 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 26 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.37 2.49 35.6 2.39e-9 6.66e-5 AT3G… BHLH039
2 2 BraA… -1.38 1.82 31.6 1.93e-8 2.20e-4 AT3G… BHLH039
3 3 BraA… -0.754 7.44 31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A
4 4 BraA… -0.648 6.87 28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A
5 5 BraA… -0.600 5.31 27.9 1.30e-7 7.24e-4 AT4G… UGT73B1
6 6 BraA… -0.616 5.60 27.0 2.02e-7 9.37e-4 AT4G… UGT73B1
7 7 BraA… 1.21 2.58 26.2 3.10e-7 1.04e-3 AT1G… TAR4
8 8 BraA… -0.831 5.65 26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1
9 9 BraA… 1.69 3.06 26.0 3.37e-7 1.04e-3 AT1G… <NA>
10 10 BraA… -1.10 7.15 24.8 6.25e-7 1.74e-3 AT1G… <NA>
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 26 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.37 2.49 35.6 2.39e-9 6.66e-5 AT3G… BHLH039
2 2 BraA… -1.38 1.82 31.6 1.93e-8 2.20e-4 AT3G… BHLH039
3 3 BraA… -0.754 7.44 31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A
4 4 BraA… -0.648 6.87 28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A
5 5 BraA… -0.600 5.31 27.9 1.30e-7 7.24e-4 AT4G… UGT73B1
6 6 BraA… -0.616 5.60 27.0 2.02e-7 9.37e-4 AT4G… UGT73B1
7 7 BraA… 1.21 2.58 26.2 3.10e-7 1.04e-3 AT1G… TAR4
8 8 BraA… -0.831 5.65 26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1
9 9 BraA… 1.69 3.06 26.0 3.37e-7 1.04e-3 AT1G… <NA>
10 10 BraA… -1.10 7.15 24.8 6.25e-7 1.74e-3 AT1G… <NA>
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
# perc_ID <dbl>
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 608 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.45 0.859 5.65 53.8 2.04e-12
2 2 BraA… -1.55 0.526 2.79 53.2 2.87e-12
3 3 BraA… -0.697 -1.05 7.15 44.3 2.45e-10
4 4 BraA… -0.663 -0.389 7.44 42.9 4.75e-10
5 5 BraA… -0.556 -0.349 6.87 38.8 3.76e- 9
6 6 BraA… 1.06 1.83 1.59 38.6 4.18e- 9
7 7 BraA… 1.73 -0.931 2.16 38.6 4.25e- 9
8 8 BraA… 0.900 0.654 3.16 37.9 5.79e- 9
9 9 BraA… 0.946 1.34 5.01 36.4 1.23e- 8
10 10 BraA… 0.527 0.753 4.69 35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 77 x 12
X1 genes logFC.trt5E_live logFC.genotypeF… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.538 -1.21 7.15 41.7 8.66e-10
2 2 BraA… -1.14 0.590 5.65 35.9 1.59e- 8
3 3 BraA… -1.50 0.191 2.49 35.1 2.43e- 8
4 4 BraA… -0.581 -0.358 7.44 33.9 4.30e- 8
5 5 BraA… 2.22 -2.33 1.23 33.7 4.91e- 8
6 6 BraA… 1.57 -1.36 4.01 31.8 1.26e- 7
7 7 BraA… -0.836 -1.91 0.848 31.7 1.32e- 7
8 8 BraA… -1.58 0.333 1.82 31.2 1.66e- 7
9 9 BraA… -0.529 -0.246 6.87 30.4 2.55e- 7
10 10 BraA… 1.69 -1.46 3.49 29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 4 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -4.86 4.91 25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2 2 BraA… 3.42 0.428 25.7 3.93e-7 0.00548 AT5G… <NA>
3 3 BraA… -1.55 1.93 20.4 6.29e-6 0.0453 AT4G… UBC17
4 4 BraA… 2.02 6.68 20.3 6.50e-6 0.0453 AT4G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 3.28 1.39 23.8 1.05e-6 0.0293 AT3G… <NA>
2 2 BraA… 2.95 0.428 21.5 3.55e-6 0.0495 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 608 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.590 -0.859 5.65 53.8 2.04e-12
2 2 BraA… -1.03 -0.526 2.79 53.2 2.87e-12
3 3 BraA… -1.74 1.05 7.15 44.3 2.45e-10
4 4 BraA… -1.05 0.389 7.44 42.9 4.75e-10
5 5 BraA… -0.905 0.349 6.87 38.8 3.76e- 9
6 6 BraA… 2.89 -1.83 1.59 38.6 4.18e- 9
7 7 BraA… 0.799 0.931 2.16 38.6 4.25e- 9
8 8 BraA… 1.55 -0.654 3.16 37.9 5.79e- 9
9 9 BraA… 2.29 -1.34 5.01 36.4 1.23e- 8
10 10 BraA… 1.28 -0.753 4.69 35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 77 x 12
X1 genes logFC.trt5E_live logFC.genotypeR… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.75 1.21 7.15 41.7 8.66e-10
2 2 BraA… -0.554 -0.590 5.65 35.9 1.59e- 8
3 3 BraA… -1.31 -0.191 2.49 35.1 2.43e- 8
4 4 BraA… -0.939 0.358 7.44 33.9 4.30e- 8
5 5 BraA… -0.113 2.33 1.23 33.7 4.91e- 8
6 6 BraA… 0.211 1.36 4.01 31.8 1.26e- 7
7 7 BraA… -2.75 1.91 0.848 31.7 1.32e- 7
8 8 BraA… -1.25 -0.333 1.82 31.2 1.66e- 7
9 9 BraA… -0.775 0.246 6.87 30.4 2.55e- 7
10 10 BraA… 0.236 1.46 3.49 29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 4 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 4.86 4.91 25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2 2 BraA… -3.42 0.428 25.7 3.93e-7 0.00548 AT5G… <NA>
3 3 BraA… 1.55 1.93 20.4 6.29e-6 0.0453 AT4G… UBC17
4 4 BraA… -2.02 6.68 20.3 6.50e-6 0.0453 AT4G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
# confirm
DEG.count.list.e1.v3.0annotation.all.FDR0.05[["root.R500.trtlive.DEGs.all.rD.v3.0anno"]] %>% View() # OK. 383 genes
# Reading DEGs list exp3
# all model including subset data
DEG.objs.e3.v3.0annotation.all<-list.files(path=file.path("..","v3.0annotation","20180202-samples","output","FULLtoptag"),
pattern="(^leaf|^root)(\\.)(.+)(v3.0anno)(.csv)")
# read csv file (only full model)
DEG.count.list.e3.v3.0annotation.all<-lapply(DEG.objs.e3.v3.0annotation.all, function(x) read_csv(paste(file.path("..","v3.0annotation","20180202-samples","output","FULLtoptag"),"/",x,sep="")))
names(DEG.count.list.e3.v3.0annotation.all)<-gsub(".csv","",DEG.objs.e3.v3.0annotation.all)
DEG.count.list.e3.v3.0annotation.all[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05)
# A tibble: 3,887 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.96 4.70 87.7 7.54e-21 1.07e-16 AT1G… ASP4
2 2 BraA… 1.22 5.63 87.6 8.17e-21 1.07e-16 AT2G… <NA>
3 3 BraA… 1.28 5.28 83.6 6.07e-20 5.29e-16 AT1G… BRR2
4 4 BraA… -1.15 5.99 81.6 1.70e-19 1.11e-15 AT2G… <NA>
5 5 BraA… 1.14 7.09 75.2 4.17e-18 2.18e-14 AT1G… BRR2
6 6 BraA… 1.02 5.44 74.1 7.24e-18 3.16e-14 AT5G… <NA>
7 7 BraA… 1.94 3.77 71.4 2.91e-17 1.09e-13 AT3G… TIC
8 8 BraA… 0.928 7.49 69.8 6.47e-17 2.03e-13 AT2G… ATGSL03
9 9 BraA… 1.59 3.73 69.7 6.98e-17 2.03e-13 AT1G… ASU1
10 10 BraA… 1.30 3.72 66.9 2.79e-16 7.10e-13 AT5G… <NA>
# ... with 3,877 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
names(DEG.count.list.e3.v3.0annotation.all)
[1] "leaf.cr.trtlive.DEGs.all.rD.v3.0anno"
[2] "leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[3] "leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[4] "leaf.densitycr.DEGs.add.rD.rUN.v3.0anno"
[5] "leaf.densitycr.DEGs.add.rL.rUN.v3.0anno"
[6] "leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[7] "leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[8] "leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[9] "leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[10] "leaf.densityun.DEGs.add.rD.rCR.v3.0anno"
[11] "leaf.densityun.DEGs.add.rL.rCR.v3.0anno"
[12] "leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[13] "leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[14] "leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[15] "leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[16] "leaf.trtdead.DEGs.add.rL.rCR.v3.0anno"
[17] "leaf.trtdead.DEGs.add.rL.rUN.v3.0anno"
[18] "leaf.trtdead.DEGs.int.rL.rCR.v3.0anno"
[19] "leaf.trtdead.DEGs.int.rL.rUN.v3.0anno"
[20] "leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[21] "leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[22] "leaf.trtlive.DEGs.add.rD.rCR.v3.0anno"
[23] "leaf.trtlive.DEGs.add.rD.rUN.v3.0anno"
[24] "leaf.trtlive.DEGs.int.rD.rCR.v3.0anno"
[25] "leaf.trtlive.DEGs.int.rD.rUN.v3.0anno"
[26] "leaf.un.trtlive.DEGs.all.rD.v3.0anno"
[27] "root.cr.trtlive.DEGs.all.rD.v3.0anno"
[28] "root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[29] "root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[30] "root.densitycr.DEGs.add.rD.rUN.v3.0anno"
[31] "root.densitycr.DEGs.add.rL.rUN.v3.0anno"
[32] "root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[33] "root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[34] "root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[35] "root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[36] "root.densityun.DEGs.add.rD.rCR.v3.0anno"
[37] "root.densityun.DEGs.add.rL.rCR.v3.0anno"
[38] "root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[39] "root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[40] "root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[41] "root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[42] "root.trtdead.DEGs.add.rL.rCR.v3.0anno"
[43] "root.trtdead.DEGs.add.rL.rUN.v3.0anno"
[44] "root.trtdead.DEGs.int.rL.rCR.v3.0anno"
[45] "root.trtdead.DEGs.int.rL.rUN.v3.0anno"
[46] "root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[47] "root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[48] "root.trtlive.DEGs.add.rD.rCR.v3.0anno"
[49] "root.trtlive.DEGs.add.rD.rUN.v3.0anno"
[50] "root.trtlive.DEGs.int.rD.rCR.v3.0anno"
[51] "root.trtlive.DEGs.int.rD.rUN.v3.0anno"
[52] "root.un.trtlive.DEGs.all.rD.v3.0anno"
# FDR<0.05
DEG.count.list.e3.v3.0annotation.all %>% map(filter(FDR<0.05)) # does not work
Error in filter(FDR < 0.05): object 'FDR' not found
DEG.count.list.e3.v3.0annotation.all.FDR0.05<-DEG.count.list.e3.v3.0annotation.all %>% map(function(df) filter(df,FDR<0.05)) # does work
names(DEG.count.list.e3.v3.0annotation.all.FDR0.05)
[1] "leaf.cr.trtlive.DEGs.all.rD.v3.0anno"
[2] "leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[3] "leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[4] "leaf.densitycr.DEGs.add.rD.rUN.v3.0anno"
[5] "leaf.densitycr.DEGs.add.rL.rUN.v3.0anno"
[6] "leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[7] "leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[8] "leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[9] "leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[10] "leaf.densityun.DEGs.add.rD.rCR.v3.0anno"
[11] "leaf.densityun.DEGs.add.rL.rCR.v3.0anno"
[12] "leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[13] "leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[14] "leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[15] "leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[16] "leaf.trtdead.DEGs.add.rL.rCR.v3.0anno"
[17] "leaf.trtdead.DEGs.add.rL.rUN.v3.0anno"
[18] "leaf.trtdead.DEGs.int.rL.rCR.v3.0anno"
[19] "leaf.trtdead.DEGs.int.rL.rUN.v3.0anno"
[20] "leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[21] "leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[22] "leaf.trtlive.DEGs.add.rD.rCR.v3.0anno"
[23] "leaf.trtlive.DEGs.add.rD.rUN.v3.0anno"
[24] "leaf.trtlive.DEGs.int.rD.rCR.v3.0anno"
[25] "leaf.trtlive.DEGs.int.rD.rUN.v3.0anno"
[26] "leaf.un.trtlive.DEGs.all.rD.v3.0anno"
[27] "root.cr.trtlive.DEGs.all.rD.v3.0anno"
[28] "root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[29] "root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[30] "root.densitycr.DEGs.add.rD.rUN.v3.0anno"
[31] "root.densitycr.DEGs.add.rL.rUN.v3.0anno"
[32] "root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[33] "root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[34] "root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[35] "root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[36] "root.densityun.DEGs.add.rD.rCR.v3.0anno"
[37] "root.densityun.DEGs.add.rL.rCR.v3.0anno"
[38] "root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[39] "root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[40] "root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[41] "root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[42] "root.trtdead.DEGs.add.rL.rCR.v3.0anno"
[43] "root.trtdead.DEGs.add.rL.rUN.v3.0anno"
[44] "root.trtdead.DEGs.int.rL.rCR.v3.0anno"
[45] "root.trtdead.DEGs.int.rL.rUN.v3.0anno"
[46] "root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[47] "root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[48] "root.trtlive.DEGs.add.rD.rCR.v3.0anno"
[49] "root.trtlive.DEGs.add.rD.rUN.v3.0anno"
[50] "root.trtlive.DEGs.int.rD.rCR.v3.0anno"
[51] "root.trtlive.DEGs.int.rD.rUN.v3.0anno"
[52] "root.un.trtlive.DEGs.all.rD.v3.0anno"
# alternative way
DEG.count.list.e3.v3.0annotation.all %>% map(~filter(.,FDR<0.05)) # does work
$leaf.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 12 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.75 2.86 20.6 5.77e-6 0.0413 AT1G… <NA>
2 2 BraA… 1.05 8.17 19.2 1.19e-5 0.0413 AT5G… AtHsp90-3
3 3 BraA… -3.07 0.296 18.7 1.49e-5 0.0413 AT2G… PLAT2
4 4 BraA… 2.69 0.508 18.7 1.50e-5 0.0413 AT1G… <NA>
5 5 BraA… -0.961 7.30 18.7 1.51e-5 0.0413 AT1G… AtPMT3
6 6 BraA… 1.64 3.71 18.7 1.51e-5 0.0413 AT5G… AAP4
7 7 BraA… 1.66 2.15 18.7 1.54e-5 0.0413 AT2G… ArathEUL…
8 8 BraA… -0.846 4.97 18.5 1.71e-5 0.0413 AT4G… ATCAD7
9 9 BraA… 1.68 3.95 18.3 1.89e-5 0.0413 AT5G… <NA>
10 10 BraA… 2.83 1.000 18.3 1.91e-5 0.0413 AT5G… ANAC092
11 11 BraA… 2.35 2.04 18.2 1.94e-5 0.0413 AT5G… <NA>
12 12 BraA… 1.67 2.20 17.8 2.40e-5 0.0469 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -7.74 1.09 4.09 891. 2.88e-194
2 2 BraA… -2.65 0.0205 8.15 664. 7.63e-145
3 3 BraA… -2.66 -0.00762 7.37 574. 1.78e-125
4 4 BraA… 3.98 0.267 7.24 510. 1.56e-111
5 5 BraA… -4.47 0.399 7.29 494. 6.31e-108
6 6 BraA… -2.65 0.139 7.53 491. 1.88e-107
7 7 BraA… -2.11 -0.281 6.87 477. 2.91e-104
8 8 BraA… -3.09 0.124 5.97 471. 5.85e-103
9 9 BraA… -3.07 -0.179 7.57 470. 7.61e-103
10 10 BraA… -2.45 -0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -6.65 -1.09 4.09 891. 2.88e-194
2 2 BraA… -2.63 -0.0205 8.15 664. 7.63e-145
3 3 BraA… -2.67 0.00762 7.37 574. 1.78e-125
4 4 BraA… 4.25 -0.267 7.24 510. 1.56e-111
5 5 BraA… -4.07 -0.399 7.29 494. 6.31e-108
6 6 BraA… -2.51 -0.139 7.53 491. 1.88e-107
7 7 BraA… -2.39 0.281 6.87 477. 2.91e-104
8 8 BraA… -2.97 -0.124 5.97 471. 5.85e-103
9 9 BraA… -3.25 0.179 7.57 470. 7.61e-103
10 10 BraA… -2.55 0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… -2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… -2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… 4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… -2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… -4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… -3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… -2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… -3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… -2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… -2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… -2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… 4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… -2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… -4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… -3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… -2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… -3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… -2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… -3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… 3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 7.74 -1.09 4.09 891. 2.88e-194
2 2 BraA… 2.65 -0.0205 8.15 664. 7.63e-145
3 3 BraA… 2.66 0.00762 7.37 574. 1.78e-125
4 4 BraA… -3.98 -0.267 7.24 510. 1.56e-111
5 5 BraA… 4.47 -0.399 7.29 494. 6.31e-108
6 6 BraA… 2.65 -0.139 7.53 491. 1.88e-107
7 7 BraA… 2.11 0.281 6.87 477. 2.91e-104
8 8 BraA… 3.09 -0.124 5.97 471. 5.85e-103
9 9 BraA… 3.07 0.179 7.57 470. 7.61e-103
10 10 BraA… 2.45 0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 6.65 1.09 4.09 891. 2.88e-194
2 2 BraA… 2.63 0.0205 8.15 664. 7.63e-145
3 3 BraA… 2.67 -0.00762 7.37 574. 1.78e-125
4 4 BraA… -4.25 0.267 7.24 510. 1.56e-111
5 5 BraA… 4.07 0.399 7.29 494. 6.31e-108
6 6 BraA… 2.51 0.139 7.53 491. 1.88e-107
7 7 BraA… 2.39 -0.281 6.87 477. 2.91e-104
8 8 BraA… 2.97 0.124 5.97 471. 5.85e-103
9 9 BraA… 3.25 -0.179 7.57 470. 7.61e-103
10 10 BraA… 2.55 -0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… 2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… 2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… -4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… 2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… 4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… 3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… 2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… 3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… 2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… 2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… 2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… -4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… 2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… 4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… 3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… 2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… 3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… 2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 2 x 12
X1 genes logFC logCPM LR PValue FDR X1_1 AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr> <chr>
1 1 BraA… 2.00 4.58 22.9 1.69e-6 0.0271 23774 AT1G… ARR7
2 2 BraA… 3.95 0.659 22.3 2.27e-6 0.0271 33024 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… -3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtdead logFC.densitycr… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.276 -0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… -0.489 -0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… 0.758 2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… 0.189 0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… -0.0786 -1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… 0.192 0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… 0.124 1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… 1.25 -3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… 0.0242 -1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… 0.916 -2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtdead logFC.densityun… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.04 0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… -0.865 0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… 2.90 -2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… 0.903 -0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… -1.30 1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… 0.964 -0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… 1.27 -1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… -2.70 3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… -1.67 1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… -1.09 2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… -0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… -1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… -0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… -1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 370 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.04 7.58 27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
2 2 BraA… -1.30 5.52 24.7 6.80e-7 0.00491 AT2G… <NA>
3 3 BraA… 1.27 4.46 23.8 1.06e-6 0.00491 AT1G… HHO6
4 4 BraA… 0.903 4.94 23.8 1.07e-6 0.00491 AT4G… PDE327
5 5 BraA… 0.964 4.89 23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
6 6 BraA… -1.67 3.11 23.5 1.23e-6 0.00491 AT5G… <NA>
7 7 BraA… 0.856 4.77 22.5 2.13e-6 0.00727 AT4G… ATCAD7
8 8 BraA… 2.90 0.654 21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
9 9 BraA… 0.938 7.04 21.6 3.29e-6 0.00857 AT1G… AtPMT3
10 10 BraA… -0.865 4.13 21.5 3.59e-6 0.00857 AT5G… <NA>
# ... with 360 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtlive logFC.densitycr… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.276 0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… 0.489 0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… -0.758 -2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… -0.189 -0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… 0.0786 1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… -0.192 -0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… -0.124 -1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… -1.25 3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… -0.0242 1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… -0.916 2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtlive logFC.densityun… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.04 -0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… 0.865 -0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… -2.90 2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… -0.903 0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… 1.30 -1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… -0.964 0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… -1.27 1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… 2.70 -3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… 1.67 -1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… 1.09 -2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… 0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… 1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… 0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… 1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 370 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.04 7.58 27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
2 2 BraA… 1.30 5.52 24.7 6.80e-7 0.00491 AT2G… <NA>
3 3 BraA… -1.27 4.46 23.8 1.06e-6 0.00491 AT1G… HHO6
4 4 BraA… -0.903 4.94 23.8 1.07e-6 0.00491 AT4G… PDE327
5 5 BraA… -0.964 4.89 23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
6 6 BraA… 1.67 3.11 23.5 1.23e-6 0.00491 AT5G… <NA>
7 7 BraA… -0.856 4.77 22.5 2.13e-6 0.00727 AT4G… ATCAD7
8 8 BraA… -2.90 0.654 21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
9 9 BraA… -0.938 7.04 21.6 3.29e-6 0.00857 AT1G… AtPMT3
10 10 BraA… 0.865 4.13 21.5 3.59e-6 0.00857 AT5G… <NA>
# ... with 360 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$root.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 3,887 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.96 4.70 87.7 7.54e-21 1.07e-16 AT1G… ASP4
2 2 BraA… 1.22 5.63 87.6 8.17e-21 1.07e-16 AT2G… <NA>
3 3 BraA… 1.28 5.28 83.6 6.07e-20 5.29e-16 AT1G… BRR2
4 4 BraA… -1.15 5.99 81.6 1.70e-19 1.11e-15 AT2G… <NA>
5 5 BraA… 1.14 7.09 75.2 4.17e-18 2.18e-14 AT1G… BRR2
6 6 BraA… 1.02 5.44 74.1 7.24e-18 3.16e-14 AT5G… <NA>
7 7 BraA… 1.94 3.77 71.4 2.91e-17 1.09e-13 AT3G… TIC
8 8 BraA… 0.928 7.49 69.8 6.47e-17 2.03e-13 AT2G… ATGSL03
9 9 BraA… 1.59 3.73 69.7 6.98e-17 2.03e-13 AT1G… ASU1
10 10 BraA… 1.30 3.72 66.9 2.79e-16 7.10e-13 AT5G… <NA>
# ... with 3,877 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.88 0.498 5.32 778. 1.17e-169
2 2 BraA… 2.50 -0.287 4.42 511. 1.05e-111
3 3 BraA… -3.53 1.22 6.17 491. 2.16e-107
4 4 BraA… -3.95 1.12 4.01 486. 2.51e-106
5 5 BraA… -4.44 -0.0881 4.23 454. 2.05e- 99
6 6 BraA… -2.58 0.467 6.28 445. 2.56e- 97
7 7 BraA… 2.08 -0.172 7.33 441. 2.06e- 96
8 8 BraA… 3.07 0.696 4.36 421. 4.47e- 92
9 9 BraA… -3.22 0.782 5.90 383. 5.42e- 84
10 10 BraA… -2.31 0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.38 -0.498 5.32 778. 1.17e-169
2 2 BraA… 2.21 0.287 4.42 511. 1.05e-111
3 3 BraA… -2.31 -1.22 6.17 491. 2.16e-107
4 4 BraA… -2.83 -1.12 4.01 486. 2.51e-106
5 5 BraA… -4.53 0.0881 4.23 454. 2.05e- 99
6 6 BraA… -2.11 -0.467 6.28 445. 2.56e- 97
7 7 BraA… 1.90 0.172 7.33 441. 2.06e- 96
8 8 BraA… 3.76 -0.696 4.36 421. 4.47e- 92
9 9 BraA… -2.44 -0.782 5.90 383. 5.42e- 84
10 10 BraA… -1.62 -0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… 2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… -4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… 1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… -2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… 3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… 6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… -2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… 2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… -3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… 2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… -4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… 1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… -2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… 3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… 6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… -2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… 2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… -3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… 1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… 1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… 3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… 1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… 3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… 3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… 1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… 2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… 1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… -1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… -1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… -3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… -1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… -3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… -3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… -1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… -2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… -1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.88 -0.498 5.32 778. 1.17e-169
2 2 BraA… -2.50 0.287 4.42 511. 1.05e-111
3 3 BraA… 3.53 -1.22 6.17 491. 2.16e-107
4 4 BraA… 3.95 -1.12 4.01 486. 2.51e-106
5 5 BraA… 4.44 0.0881 4.23 454. 2.05e- 99
6 6 BraA… 2.58 -0.467 6.28 445. 2.56e- 97
7 7 BraA… -2.08 0.172 7.33 441. 2.06e- 96
8 8 BraA… -3.07 -0.696 4.36 421. 4.47e- 92
9 9 BraA… 3.22 -0.782 5.90 383. 5.42e- 84
10 10 BraA… 2.31 -0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.38 0.498 5.32 778. 1.17e-169
2 2 BraA… -2.21 -0.287 4.42 511. 1.05e-111
3 3 BraA… 2.31 1.22 6.17 491. 2.16e-107
4 4 BraA… 2.83 1.12 4.01 486. 2.51e-106
5 5 BraA… 4.53 -0.0881 4.23 454. 2.05e- 99
6 6 BraA… 2.11 0.467 6.28 445. 2.56e- 97
7 7 BraA… -1.90 -0.172 7.33 441. 2.06e- 96
8 8 BraA… -3.76 0.696 4.36 421. 4.47e- 92
9 9 BraA… 2.44 0.782 5.90 383. 5.42e- 84
10 10 BraA… 1.62 0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… -2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… 4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… -1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… 2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… -3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… -6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… 2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… -2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… 3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… -2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… 4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… -1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… 2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… -3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… -6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… 2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… -2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… 3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 471 x 12
X1 genes logFC logCPM LR PValue FDR X1_1 AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr> <chr>
1 1 BraA… -2.06 4.03 41.3 1.28e-10 3.36e-6 15390 AT3G… BHLH039
2 2 BraA… -1.60 5.88 36.8 1.33e- 9 1.75e-5 35547 AT1G… ASP4
3 3 BraA… -1.11 6.78 32.4 1.27e- 8 1.12e-4 23863 AT1G… ATSBT5.2
4 4 BraA… -3.40 5.12 28.1 1.13e- 7 7.45e-4 4032 AT3G… <NA>
5 5 BraA… -1.50 4.22 26.7 2.33e- 7 1.14e-3 1149 AT4G… ATIRT1
6 6 BraA… -3.19 2.39 26.5 2.60e- 7 1.14e-3 39482 AT1G… GAT
7 7 BraA… -3.72 0.831 24.9 6.10e- 7 2.10e-3 28198 AT5G… <NA>
8 8 BraA… -1.72 5.26 24.8 6.39e- 7 2.10e-3 14171 AT5G… AtCOMT
9 9 BraA… -2.14 5.04 24.0 9.43e- 7 2.76e-3 21279 AT3G… F6'H1
10 10 BraA… -1.84 4.05 23.8 1.08e- 6 2.84e-3 771 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… 1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… 1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… 3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… 1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… 3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… 3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… 1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… 2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… 1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtdead logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.370 1.60 5.88 105. 1.40e-23
2 2 BraA… 0.0552 2.06 4.03 77.8 1.27e-17
3 3 BraA… 0.372 0.682 6.91 73.4 1.16e-16
4 4 BraA… 0.211 1.50 4.22 65.5 5.99e-15
5 5 BraA… -0.523 -0.132 8.54 63.6 1.56e-14
6 6 BraA… -0.331 -0.590 7.24 60.6 6.97e-14
7 7 BraA… -2.20 1.84 2.44 59.1 1.50e-13
8 8 BraA… -2.52 1.41 1.76 58.1 2.36e-13
9 9 BraA… -0.128 -0.895 5.25 56.8 4.62e-13
10 10 BraA… -0.231 -0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtdead logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.97 -1.60 5.88 105. 1.40e-23
2 2 BraA… 2.11 -2.06 4.03 77.8 1.27e-17
3 3 BraA… 1.05 -0.682 6.91 73.4 1.16e-16
4 4 BraA… 1.71 -1.50 4.22 65.5 5.99e-15
5 5 BraA… -0.655 0.132 8.54 63.6 1.56e-14
6 6 BraA… -0.921 0.590 7.24 60.6 6.97e-14
7 7 BraA… -0.353 -1.84 2.44 59.1 1.50e-13
8 8 BraA… -1.12 -1.41 1.76 58.1 2.36e-13
9 9 BraA… -1.02 0.895 5.25 56.8 4.62e-13
10 10 BraA… -1.22 0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… 2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… 1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… 0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… -1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… 0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… -0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… -0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… 0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… -0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… 2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… 1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… 0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… -1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… 0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… -0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… -0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… 0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… -0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,434 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.97 5.88 101. 9.26e-24 2.44e-19 AT1G… ASP4
2 2 BraA… 2.11 4.03 77.7 1.18e-18 1.55e-14 AT3G… BHLH039
3 3 BraA… 1.05 6.91 65.1 7.00e-16 6.15e-12 AT1G… ATOPR2
4 4 BraA… 1.71 4.22 64.3 1.05e-15 6.92e-12 AT4G… ATIRT1
5 5 BraA… -1.02 5.25 55.9 7.52e-14 3.96e-10 AT5G… <NA>
6 6 BraA… -0.921 7.24 53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03
7 7 BraA… -1.22 5.48 53.3 2.83e-13 1.07e- 9 AT2G… <NA>
8 8 BraA… 1.81 5.26 51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT
9 9 BraA… 1.16 5.96 50.9 9.52e-13 2.30e- 9 AT2G… <NA>
10 10 BraA… -1.24 3.91 50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F
# ... with 3,424 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 357 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.20 2.44 57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12
2 2 BraA… -2.52 1.76 47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59
3 3 BraA… -4.03 0.831 46.6 8.91e-12 7.82e- 8 AT5G… <NA>
4 4 BraA… -1.40 3.53 41.0 1.52e-10 1.00e- 6 AT1G… HMS
5 5 BraA… -1.35 2.35 38.1 6.87e-10 3.27e- 6 AT2G… ANAC042
6 6 BraA… -2.08 3.27 37.9 7.45e-10 3.27e- 6 AT2G… <NA>
7 7 BraA… -1.97 5.83 34.1 5.13e- 9 1.93e- 5 AT4G… <NA>
8 8 BraA… -0.925 4.26 32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1
9 9 BraA… -1.86 2.87 32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042
10 10 BraA… -1.90 1.61 31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2
# ... with 347 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtlive logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.370 -1.60 5.88 105. 1.40e-23
2 2 BraA… -0.0552 -2.06 4.03 77.8 1.27e-17
3 3 BraA… -0.372 -0.682 6.91 73.4 1.16e-16
4 4 BraA… -0.211 -1.50 4.22 65.5 5.99e-15
5 5 BraA… 0.523 0.132 8.54 63.6 1.56e-14
6 6 BraA… 0.331 0.590 7.24 60.6 6.97e-14
7 7 BraA… 2.20 -1.84 2.44 59.1 1.50e-13
8 8 BraA… 2.52 -1.41 1.76 58.1 2.36e-13
9 9 BraA… 0.128 0.895 5.25 56.8 4.62e-13
10 10 BraA… 0.231 0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtlive logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.97 1.60 5.88 105. 1.40e-23
2 2 BraA… -2.11 2.06 4.03 77.8 1.27e-17
3 3 BraA… -1.05 0.682 6.91 73.4 1.16e-16
4 4 BraA… -1.71 1.50 4.22 65.5 5.99e-15
5 5 BraA… 0.655 -0.132 8.54 63.6 1.56e-14
6 6 BraA… 0.921 -0.590 7.24 60.6 6.97e-14
7 7 BraA… 0.353 1.84 2.44 59.1 1.50e-13
8 8 BraA… 1.12 1.41 1.76 58.1 2.36e-13
9 9 BraA… 1.02 -0.895 5.25 56.8 4.62e-13
10 10 BraA… 1.22 -0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… -2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… -1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… -0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… 1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… -0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… 0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… 0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… -0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… 0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… -2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… -1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… -0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… 1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… -0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… 0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… 0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… -0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… 0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,434 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.97 5.88 101. 9.26e-24 2.44e-19 AT1G… ASP4
2 2 BraA… -2.11 4.03 77.7 1.18e-18 1.55e-14 AT3G… BHLH039
3 3 BraA… -1.05 6.91 65.1 7.00e-16 6.15e-12 AT1G… ATOPR2
4 4 BraA… -1.71 4.22 64.3 1.05e-15 6.92e-12 AT4G… ATIRT1
5 5 BraA… 1.02 5.25 55.9 7.52e-14 3.96e-10 AT5G… <NA>
6 6 BraA… 0.921 7.24 53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03
7 7 BraA… 1.22 5.48 53.3 2.83e-13 1.07e- 9 AT2G… <NA>
8 8 BraA… -1.81 5.26 51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT
9 9 BraA… -1.16 5.96 50.9 9.52e-13 2.30e- 9 AT2G… <NA>
10 10 BraA… 1.24 3.91 50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F
# ... with 3,424 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 357 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.20 2.44 57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12
2 2 BraA… 2.52 1.76 47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59
3 3 BraA… 4.03 0.831 46.6 8.91e-12 7.82e- 8 AT5G… <NA>
4 4 BraA… 1.40 3.53 41.0 1.52e-10 1.00e- 6 AT1G… HMS
5 5 BraA… 1.35 2.35 38.1 6.87e-10 3.27e- 6 AT2G… ANAC042
6 6 BraA… 2.08 3.27 37.9 7.45e-10 3.27e- 6 AT2G… <NA>
7 7 BraA… 1.97 5.83 34.1 5.13e- 9 1.93e- 5 AT4G… <NA>
8 8 BraA… 0.925 4.26 32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1
9 9 BraA… 1.86 2.87 32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042
10 10 BraA… 1.90 1.61 31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2
# ... with 347 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 297 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.19 2.37 56.7 5.00e-14 1.30e-9 AT1G… ATGSTU12
2 2 BraA… 2.06 3.30 47.4 5.87e-12 5.83e-8 AT2G… <NA>
3 3 BraA… 4.05 0.567 47.1 6.75e-12 5.83e-8 AT5G… <NA>
4 4 BraA… 2.52 1.68 46.1 1.13e-11 7.29e-8 AT2G… ATWRKY59
5 5 BraA… -2.17 1.80 45.7 1.41e-11 7.32e-8 AT2G… <NA>
6 6 BraA… 1.41 2.87 43.4 4.55e-11 1.97e-7 AT1G… HMS
7 7 BraA… 1.86 2.20 38.3 5.95e-10 2.20e-6 AT2G… ANAC042
8 8 BraA… 0.933 4.20 38.0 7.03e-10 2.28e-6 AT4G… CYP706A1
9 9 BraA… 1.46 1.59 37.5 9.38e-10 2.70e-6 AT5G… <NA>
10 10 BraA… 1.90 1.67 36.6 1.48e- 9 3.84e-6 AT1G… IGMT2
# ... with 287 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
map(DEG.count.list.e3.v3.0annotation.all,~filter(.x,FDR<0.05)) # does work
$leaf.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 12 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.75 2.86 20.6 5.77e-6 0.0413 AT1G… <NA>
2 2 BraA… 1.05 8.17 19.2 1.19e-5 0.0413 AT5G… AtHsp90-3
3 3 BraA… -3.07 0.296 18.7 1.49e-5 0.0413 AT2G… PLAT2
4 4 BraA… 2.69 0.508 18.7 1.50e-5 0.0413 AT1G… <NA>
5 5 BraA… -0.961 7.30 18.7 1.51e-5 0.0413 AT1G… AtPMT3
6 6 BraA… 1.64 3.71 18.7 1.51e-5 0.0413 AT5G… AAP4
7 7 BraA… 1.66 2.15 18.7 1.54e-5 0.0413 AT2G… ArathEUL…
8 8 BraA… -0.846 4.97 18.5 1.71e-5 0.0413 AT4G… ATCAD7
9 9 BraA… 1.68 3.95 18.3 1.89e-5 0.0413 AT5G… <NA>
10 10 BraA… 2.83 1.000 18.3 1.91e-5 0.0413 AT5G… ANAC092
11 11 BraA… 2.35 2.04 18.2 1.94e-5 0.0413 AT5G… <NA>
12 12 BraA… 1.67 2.20 17.8 2.40e-5 0.0469 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -7.74 1.09 4.09 891. 2.88e-194
2 2 BraA… -2.65 0.0205 8.15 664. 7.63e-145
3 3 BraA… -2.66 -0.00762 7.37 574. 1.78e-125
4 4 BraA… 3.98 0.267 7.24 510. 1.56e-111
5 5 BraA… -4.47 0.399 7.29 494. 6.31e-108
6 6 BraA… -2.65 0.139 7.53 491. 1.88e-107
7 7 BraA… -2.11 -0.281 6.87 477. 2.91e-104
8 8 BraA… -3.09 0.124 5.97 471. 5.85e-103
9 9 BraA… -3.07 -0.179 7.57 470. 7.61e-103
10 10 BraA… -2.45 -0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -6.65 -1.09 4.09 891. 2.88e-194
2 2 BraA… -2.63 -0.0205 8.15 664. 7.63e-145
3 3 BraA… -2.67 0.00762 7.37 574. 1.78e-125
4 4 BraA… 4.25 -0.267 7.24 510. 1.56e-111
5 5 BraA… -4.07 -0.399 7.29 494. 6.31e-108
6 6 BraA… -2.51 -0.139 7.53 491. 1.88e-107
7 7 BraA… -2.39 0.281 6.87 477. 2.91e-104
8 8 BraA… -2.97 -0.124 5.97 471. 5.85e-103
9 9 BraA… -3.25 0.179 7.57 470. 7.61e-103
10 10 BraA… -2.55 0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… -2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… -2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… 4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… -2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… -4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… -3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… -2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… -3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… -2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… -2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… -2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… 4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… -2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… -4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… -3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… -2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… -3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… -2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… -3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… 3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 7.74 -1.09 4.09 891. 2.88e-194
2 2 BraA… 2.65 -0.0205 8.15 664. 7.63e-145
3 3 BraA… 2.66 0.00762 7.37 574. 1.78e-125
4 4 BraA… -3.98 -0.267 7.24 510. 1.56e-111
5 5 BraA… 4.47 -0.399 7.29 494. 6.31e-108
6 6 BraA… 2.65 -0.139 7.53 491. 1.88e-107
7 7 BraA… 2.11 0.281 6.87 477. 2.91e-104
8 8 BraA… 3.09 -0.124 5.97 471. 5.85e-103
9 9 BraA… 3.07 0.179 7.57 470. 7.61e-103
10 10 BraA… 2.45 0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 6.65 1.09 4.09 891. 2.88e-194
2 2 BraA… 2.63 0.0205 8.15 664. 7.63e-145
3 3 BraA… 2.67 -0.00762 7.37 574. 1.78e-125
4 4 BraA… -4.25 0.267 7.24 510. 1.56e-111
5 5 BraA… 4.07 0.399 7.29 494. 6.31e-108
6 6 BraA… 2.51 0.139 7.53 491. 1.88e-107
7 7 BraA… 2.39 -0.281 6.87 477. 2.91e-104
8 8 BraA… 2.97 0.124 5.97 471. 5.85e-103
9 9 BraA… 3.25 -0.179 7.57 470. 7.61e-103
10 10 BraA… 2.55 -0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… 2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… 2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… -4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… 2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… 4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… 3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… 2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… 3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… 2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… 2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… 2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… -4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… 2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… 4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… 3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… 2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… 3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… 2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 2 x 12
X1 genes logFC logCPM LR PValue FDR X1_1 AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr> <chr>
1 1 BraA… 2.00 4.58 22.9 1.69e-6 0.0271 23774 AT1G… ARR7
2 2 BraA… 3.95 0.659 22.3 2.27e-6 0.0271 33024 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… -3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtdead logFC.densitycr… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.276 -0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… -0.489 -0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… 0.758 2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… 0.189 0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… -0.0786 -1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… 0.192 0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… 0.124 1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… 1.25 -3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… 0.0242 -1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… 0.916 -2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtdead logFC.densityun… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.04 0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… -0.865 0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… 2.90 -2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… 0.903 -0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… -1.30 1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… 0.964 -0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… 1.27 -1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… -2.70 3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… -1.67 1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… -1.09 2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… -0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… -1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… -0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… -1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 370 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.04 7.58 27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
2 2 BraA… -1.30 5.52 24.7 6.80e-7 0.00491 AT2G… <NA>
3 3 BraA… 1.27 4.46 23.8 1.06e-6 0.00491 AT1G… HHO6
4 4 BraA… 0.903 4.94 23.8 1.07e-6 0.00491 AT4G… PDE327
5 5 BraA… 0.964 4.89 23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
6 6 BraA… -1.67 3.11 23.5 1.23e-6 0.00491 AT5G… <NA>
7 7 BraA… 0.856 4.77 22.5 2.13e-6 0.00727 AT4G… ATCAD7
8 8 BraA… 2.90 0.654 21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
9 9 BraA… 0.938 7.04 21.6 3.29e-6 0.00857 AT1G… AtPMT3
10 10 BraA… -0.865 4.13 21.5 3.59e-6 0.00857 AT5G… <NA>
# ... with 360 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtlive logFC.densitycr… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.276 0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… 0.489 0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… -0.758 -2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… -0.189 -0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… 0.0786 1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… -0.192 -0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… -0.124 -1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… -1.25 3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… -0.0242 1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… -0.916 2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtlive logFC.densityun… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.04 -0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… 0.865 -0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… -2.90 2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… -0.903 0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… 1.30 -1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… -0.964 0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… -1.27 1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… 2.70 -3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… 1.67 -1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… 1.09 -2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… 0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… 1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… 0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… 1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 370 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.04 7.58 27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
2 2 BraA… 1.30 5.52 24.7 6.80e-7 0.00491 AT2G… <NA>
3 3 BraA… -1.27 4.46 23.8 1.06e-6 0.00491 AT1G… HHO6
4 4 BraA… -0.903 4.94 23.8 1.07e-6 0.00491 AT4G… PDE327
5 5 BraA… -0.964 4.89 23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
6 6 BraA… 1.67 3.11 23.5 1.23e-6 0.00491 AT5G… <NA>
7 7 BraA… -0.856 4.77 22.5 2.13e-6 0.00727 AT4G… ATCAD7
8 8 BraA… -2.90 0.654 21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
9 9 BraA… -0.938 7.04 21.6 3.29e-6 0.00857 AT1G… AtPMT3
10 10 BraA… 0.865 4.13 21.5 3.59e-6 0.00857 AT5G… <NA>
# ... with 360 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$root.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 3,887 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.96 4.70 87.7 7.54e-21 1.07e-16 AT1G… ASP4
2 2 BraA… 1.22 5.63 87.6 8.17e-21 1.07e-16 AT2G… <NA>
3 3 BraA… 1.28 5.28 83.6 6.07e-20 5.29e-16 AT1G… BRR2
4 4 BraA… -1.15 5.99 81.6 1.70e-19 1.11e-15 AT2G… <NA>
5 5 BraA… 1.14 7.09 75.2 4.17e-18 2.18e-14 AT1G… BRR2
6 6 BraA… 1.02 5.44 74.1 7.24e-18 3.16e-14 AT5G… <NA>
7 7 BraA… 1.94 3.77 71.4 2.91e-17 1.09e-13 AT3G… TIC
8 8 BraA… 0.928 7.49 69.8 6.47e-17 2.03e-13 AT2G… ATGSL03
9 9 BraA… 1.59 3.73 69.7 6.98e-17 2.03e-13 AT1G… ASU1
10 10 BraA… 1.30 3.72 66.9 2.79e-16 7.10e-13 AT5G… <NA>
# ... with 3,877 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.88 0.498 5.32 778. 1.17e-169
2 2 BraA… 2.50 -0.287 4.42 511. 1.05e-111
3 3 BraA… -3.53 1.22 6.17 491. 2.16e-107
4 4 BraA… -3.95 1.12 4.01 486. 2.51e-106
5 5 BraA… -4.44 -0.0881 4.23 454. 2.05e- 99
6 6 BraA… -2.58 0.467 6.28 445. 2.56e- 97
7 7 BraA… 2.08 -0.172 7.33 441. 2.06e- 96
8 8 BraA… 3.07 0.696 4.36 421. 4.47e- 92
9 9 BraA… -3.22 0.782 5.90 383. 5.42e- 84
10 10 BraA… -2.31 0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.38 -0.498 5.32 778. 1.17e-169
2 2 BraA… 2.21 0.287 4.42 511. 1.05e-111
3 3 BraA… -2.31 -1.22 6.17 491. 2.16e-107
4 4 BraA… -2.83 -1.12 4.01 486. 2.51e-106
5 5 BraA… -4.53 0.0881 4.23 454. 2.05e- 99
6 6 BraA… -2.11 -0.467 6.28 445. 2.56e- 97
7 7 BraA… 1.90 0.172 7.33 441. 2.06e- 96
8 8 BraA… 3.76 -0.696 4.36 421. 4.47e- 92
9 9 BraA… -2.44 -0.782 5.90 383. 5.42e- 84
10 10 BraA… -1.62 -0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… 2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… -4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… 1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… -2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… 3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… 6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… -2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… 2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… -3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… 2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… -4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… 1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… -2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… 3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… 6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… -2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… 2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… -3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… 1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… 1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… 3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… 1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… 3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… 3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… 1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… 2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… 1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… -1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… -1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… -3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… -1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… -3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… -3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… -1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… -2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… -1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.88 -0.498 5.32 778. 1.17e-169
2 2 BraA… -2.50 0.287 4.42 511. 1.05e-111
3 3 BraA… 3.53 -1.22 6.17 491. 2.16e-107
4 4 BraA… 3.95 -1.12 4.01 486. 2.51e-106
5 5 BraA… 4.44 0.0881 4.23 454. 2.05e- 99
6 6 BraA… 2.58 -0.467 6.28 445. 2.56e- 97
7 7 BraA… -2.08 0.172 7.33 441. 2.06e- 96
8 8 BraA… -3.07 -0.696 4.36 421. 4.47e- 92
9 9 BraA… 3.22 -0.782 5.90 383. 5.42e- 84
10 10 BraA… 2.31 -0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.38 0.498 5.32 778. 1.17e-169
2 2 BraA… -2.21 -0.287 4.42 511. 1.05e-111
3 3 BraA… 2.31 1.22 6.17 491. 2.16e-107
4 4 BraA… 2.83 1.12 4.01 486. 2.51e-106
5 5 BraA… 4.53 -0.0881 4.23 454. 2.05e- 99
6 6 BraA… 2.11 0.467 6.28 445. 2.56e- 97
7 7 BraA… -1.90 -0.172 7.33 441. 2.06e- 96
8 8 BraA… -3.76 0.696 4.36 421. 4.47e- 92
9 9 BraA… 2.44 0.782 5.90 383. 5.42e- 84
10 10 BraA… 1.62 0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… -2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… 4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… -1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… 2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… -3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… -6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… 2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… -2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… 3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… -2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… 4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… -1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… 2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… -3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… -6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… 2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… -2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… 3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 471 x 12
X1 genes logFC logCPM LR PValue FDR X1_1 AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr> <chr>
1 1 BraA… -2.06 4.03 41.3 1.28e-10 3.36e-6 15390 AT3G… BHLH039
2 2 BraA… -1.60 5.88 36.8 1.33e- 9 1.75e-5 35547 AT1G… ASP4
3 3 BraA… -1.11 6.78 32.4 1.27e- 8 1.12e-4 23863 AT1G… ATSBT5.2
4 4 BraA… -3.40 5.12 28.1 1.13e- 7 7.45e-4 4032 AT3G… <NA>
5 5 BraA… -1.50 4.22 26.7 2.33e- 7 1.14e-3 1149 AT4G… ATIRT1
6 6 BraA… -3.19 2.39 26.5 2.60e- 7 1.14e-3 39482 AT1G… GAT
7 7 BraA… -3.72 0.831 24.9 6.10e- 7 2.10e-3 28198 AT5G… <NA>
8 8 BraA… -1.72 5.26 24.8 6.39e- 7 2.10e-3 14171 AT5G… AtCOMT
9 9 BraA… -2.14 5.04 24.0 9.43e- 7 2.76e-3 21279 AT3G… F6'H1
10 10 BraA… -1.84 4.05 23.8 1.08e- 6 2.84e-3 771 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… 1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… 1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… 3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… 1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… 3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… 3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… 1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… 2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… 1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtdead logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.370 1.60 5.88 105. 1.40e-23
2 2 BraA… 0.0552 2.06 4.03 77.8 1.27e-17
3 3 BraA… 0.372 0.682 6.91 73.4 1.16e-16
4 4 BraA… 0.211 1.50 4.22 65.5 5.99e-15
5 5 BraA… -0.523 -0.132 8.54 63.6 1.56e-14
6 6 BraA… -0.331 -0.590 7.24 60.6 6.97e-14
7 7 BraA… -2.20 1.84 2.44 59.1 1.50e-13
8 8 BraA… -2.52 1.41 1.76 58.1 2.36e-13
9 9 BraA… -0.128 -0.895 5.25 56.8 4.62e-13
10 10 BraA… -0.231 -0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtdead logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.97 -1.60 5.88 105. 1.40e-23
2 2 BraA… 2.11 -2.06 4.03 77.8 1.27e-17
3 3 BraA… 1.05 -0.682 6.91 73.4 1.16e-16
4 4 BraA… 1.71 -1.50 4.22 65.5 5.99e-15
5 5 BraA… -0.655 0.132 8.54 63.6 1.56e-14
6 6 BraA… -0.921 0.590 7.24 60.6 6.97e-14
7 7 BraA… -0.353 -1.84 2.44 59.1 1.50e-13
8 8 BraA… -1.12 -1.41 1.76 58.1 2.36e-13
9 9 BraA… -1.02 0.895 5.25 56.8 4.62e-13
10 10 BraA… -1.22 0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… 2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… 1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… 0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… -1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… 0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… -0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… -0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… 0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… -0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… 2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… 1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… 0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… -1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… 0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… -0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… -0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… 0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… -0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,434 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.97 5.88 101. 9.26e-24 2.44e-19 AT1G… ASP4
2 2 BraA… 2.11 4.03 77.7 1.18e-18 1.55e-14 AT3G… BHLH039
3 3 BraA… 1.05 6.91 65.1 7.00e-16 6.15e-12 AT1G… ATOPR2
4 4 BraA… 1.71 4.22 64.3 1.05e-15 6.92e-12 AT4G… ATIRT1
5 5 BraA… -1.02 5.25 55.9 7.52e-14 3.96e-10 AT5G… <NA>
6 6 BraA… -0.921 7.24 53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03
7 7 BraA… -1.22 5.48 53.3 2.83e-13 1.07e- 9 AT2G… <NA>
8 8 BraA… 1.81 5.26 51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT
9 9 BraA… 1.16 5.96 50.9 9.52e-13 2.30e- 9 AT2G… <NA>
10 10 BraA… -1.24 3.91 50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F
# ... with 3,424 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 357 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.20 2.44 57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12
2 2 BraA… -2.52 1.76 47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59
3 3 BraA… -4.03 0.831 46.6 8.91e-12 7.82e- 8 AT5G… <NA>
4 4 BraA… -1.40 3.53 41.0 1.52e-10 1.00e- 6 AT1G… HMS
5 5 BraA… -1.35 2.35 38.1 6.87e-10 3.27e- 6 AT2G… ANAC042
6 6 BraA… -2.08 3.27 37.9 7.45e-10 3.27e- 6 AT2G… <NA>
7 7 BraA… -1.97 5.83 34.1 5.13e- 9 1.93e- 5 AT4G… <NA>
8 8 BraA… -0.925 4.26 32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1
9 9 BraA… -1.86 2.87 32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042
10 10 BraA… -1.90 1.61 31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2
# ... with 347 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtlive logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.370 -1.60 5.88 105. 1.40e-23
2 2 BraA… -0.0552 -2.06 4.03 77.8 1.27e-17
3 3 BraA… -0.372 -0.682 6.91 73.4 1.16e-16
4 4 BraA… -0.211 -1.50 4.22 65.5 5.99e-15
5 5 BraA… 0.523 0.132 8.54 63.6 1.56e-14
6 6 BraA… 0.331 0.590 7.24 60.6 6.97e-14
7 7 BraA… 2.20 -1.84 2.44 59.1 1.50e-13
8 8 BraA… 2.52 -1.41 1.76 58.1 2.36e-13
9 9 BraA… 0.128 0.895 5.25 56.8 4.62e-13
10 10 BraA… 0.231 0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtlive logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.97 1.60 5.88 105. 1.40e-23
2 2 BraA… -2.11 2.06 4.03 77.8 1.27e-17
3 3 BraA… -1.05 0.682 6.91 73.4 1.16e-16
4 4 BraA… -1.71 1.50 4.22 65.5 5.99e-15
5 5 BraA… 0.655 -0.132 8.54 63.6 1.56e-14
6 6 BraA… 0.921 -0.590 7.24 60.6 6.97e-14
7 7 BraA… 0.353 1.84 2.44 59.1 1.50e-13
8 8 BraA… 1.12 1.41 1.76 58.1 2.36e-13
9 9 BraA… 1.02 -0.895 5.25 56.8 4.62e-13
10 10 BraA… 1.22 -0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… -2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… -1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… -0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… 1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… -0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… 0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… 0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… -0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… 0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… -2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… -1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… -0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… 1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… -0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… 0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… 0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… -0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… 0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,434 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.97 5.88 101. 9.26e-24 2.44e-19 AT1G… ASP4
2 2 BraA… -2.11 4.03 77.7 1.18e-18 1.55e-14 AT3G… BHLH039
3 3 BraA… -1.05 6.91 65.1 7.00e-16 6.15e-12 AT1G… ATOPR2
4 4 BraA… -1.71 4.22 64.3 1.05e-15 6.92e-12 AT4G… ATIRT1
5 5 BraA… 1.02 5.25 55.9 7.52e-14 3.96e-10 AT5G… <NA>
6 6 BraA… 0.921 7.24 53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03
7 7 BraA… 1.22 5.48 53.3 2.83e-13 1.07e- 9 AT2G… <NA>
8 8 BraA… -1.81 5.26 51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT
9 9 BraA… -1.16 5.96 50.9 9.52e-13 2.30e- 9 AT2G… <NA>
10 10 BraA… 1.24 3.91 50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F
# ... with 3,424 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 357 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.20 2.44 57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12
2 2 BraA… 2.52 1.76 47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59
3 3 BraA… 4.03 0.831 46.6 8.91e-12 7.82e- 8 AT5G… <NA>
4 4 BraA… 1.40 3.53 41.0 1.52e-10 1.00e- 6 AT1G… HMS
5 5 BraA… 1.35 2.35 38.1 6.87e-10 3.27e- 6 AT2G… ANAC042
6 6 BraA… 2.08 3.27 37.9 7.45e-10 3.27e- 6 AT2G… <NA>
7 7 BraA… 1.97 5.83 34.1 5.13e- 9 1.93e- 5 AT4G… <NA>
8 8 BraA… 0.925 4.26 32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1
9 9 BraA… 1.86 2.87 32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042
10 10 BraA… 1.90 1.61 31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2
# ... with 347 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 297 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.19 2.37 56.7 5.00e-14 1.30e-9 AT1G… ATGSTU12
2 2 BraA… 2.06 3.30 47.4 5.87e-12 5.83e-8 AT2G… <NA>
3 3 BraA… 4.05 0.567 47.1 6.75e-12 5.83e-8 AT5G… <NA>
4 4 BraA… 2.52 1.68 46.1 1.13e-11 7.29e-8 AT2G… ATWRKY59
5 5 BraA… -2.17 1.80 45.7 1.41e-11 7.32e-8 AT2G… <NA>
6 6 BraA… 1.41 2.87 43.4 4.55e-11 1.97e-7 AT1G… HMS
7 7 BraA… 1.86 2.20 38.3 5.95e-10 2.20e-6 AT2G… ANAC042
8 8 BraA… 0.933 4.20 38.0 7.03e-10 2.28e-6 AT4G… CYP706A1
9 9 BraA… 1.46 1.59 37.5 9.38e-10 2.70e-6 AT5G… <NA>
10 10 BraA… 1.90 1.67 36.6 1.48e- 9 3.84e-6 AT1G… IGMT2
# ... with 287 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
lapply(DEG.count.list.e3.v3.0annotation.all,function(df) filter(df,FDR<0.05)) # does work
$leaf.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 12 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.75 2.86 20.6 5.77e-6 0.0413 AT1G… <NA>
2 2 BraA… 1.05 8.17 19.2 1.19e-5 0.0413 AT5G… AtHsp90-3
3 3 BraA… -3.07 0.296 18.7 1.49e-5 0.0413 AT2G… PLAT2
4 4 BraA… 2.69 0.508 18.7 1.50e-5 0.0413 AT1G… <NA>
5 5 BraA… -0.961 7.30 18.7 1.51e-5 0.0413 AT1G… AtPMT3
6 6 BraA… 1.64 3.71 18.7 1.51e-5 0.0413 AT5G… AAP4
7 7 BraA… 1.66 2.15 18.7 1.54e-5 0.0413 AT2G… ArathEUL…
8 8 BraA… -0.846 4.97 18.5 1.71e-5 0.0413 AT4G… ATCAD7
9 9 BraA… 1.68 3.95 18.3 1.89e-5 0.0413 AT5G… <NA>
10 10 BraA… 2.83 1.000 18.3 1.91e-5 0.0413 AT5G… ANAC092
11 11 BraA… 2.35 2.04 18.2 1.94e-5 0.0413 AT5G… <NA>
12 12 BraA… 1.67 2.20 17.8 2.40e-5 0.0469 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -7.74 1.09 4.09 891. 2.88e-194
2 2 BraA… -2.65 0.0205 8.15 664. 7.63e-145
3 3 BraA… -2.66 -0.00762 7.37 574. 1.78e-125
4 4 BraA… 3.98 0.267 7.24 510. 1.56e-111
5 5 BraA… -4.47 0.399 7.29 494. 6.31e-108
6 6 BraA… -2.65 0.139 7.53 491. 1.88e-107
7 7 BraA… -2.11 -0.281 6.87 477. 2.91e-104
8 8 BraA… -3.09 0.124 5.97 471. 5.85e-103
9 9 BraA… -3.07 -0.179 7.57 470. 7.61e-103
10 10 BraA… -2.45 -0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -6.65 -1.09 4.09 891. 2.88e-194
2 2 BraA… -2.63 -0.0205 8.15 664. 7.63e-145
3 3 BraA… -2.67 0.00762 7.37 574. 1.78e-125
4 4 BraA… 4.25 -0.267 7.24 510. 1.56e-111
5 5 BraA… -4.07 -0.399 7.29 494. 6.31e-108
6 6 BraA… -2.51 -0.139 7.53 491. 1.88e-107
7 7 BraA… -2.39 0.281 6.87 477. 2.91e-104
8 8 BraA… -2.97 -0.124 5.97 471. 5.85e-103
9 9 BraA… -3.25 0.179 7.57 470. 7.61e-103
10 10 BraA… -2.55 0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… -2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… -2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… 4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… -2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… -4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… -3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… -2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… -3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… -2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… -2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… -2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… 4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… -2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… -4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… -3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… -2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… -3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… -2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… -3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… 3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 7.74 -1.09 4.09 891. 2.88e-194
2 2 BraA… 2.65 -0.0205 8.15 664. 7.63e-145
3 3 BraA… 2.66 0.00762 7.37 574. 1.78e-125
4 4 BraA… -3.98 -0.267 7.24 510. 1.56e-111
5 5 BraA… 4.47 -0.399 7.29 494. 6.31e-108
6 6 BraA… 2.65 -0.139 7.53 491. 1.88e-107
7 7 BraA… 2.11 0.281 6.87 477. 2.91e-104
8 8 BraA… 3.09 -0.124 5.97 471. 5.85e-103
9 9 BraA… 3.07 0.179 7.57 470. 7.61e-103
10 10 BraA… 2.45 0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 14,074 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 6.65 1.09 4.09 891. 2.88e-194
2 2 BraA… 2.63 0.0205 8.15 664. 7.63e-145
3 3 BraA… 2.67 -0.00762 7.37 574. 1.78e-125
4 4 BraA… -4.25 0.267 7.24 510. 1.56e-111
5 5 BraA… 4.07 0.399 7.29 494. 6.31e-108
6 6 BraA… 2.51 0.139 7.53 491. 1.88e-107
7 7 BraA… 2.39 -0.281 6.87 477. 2.91e-104
8 8 BraA… 2.97 0.124 5.97 471. 5.85e-103
9 9 BraA… 3.25 -0.179 7.57 470. 7.61e-103
10 10 BraA… 2.55 -0.0962 4.91 467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… 2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… 2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… -4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… 2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… 4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… 3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… 2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… 3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… 2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 14,919 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 7.03 4.09 860. 5.16e-189 1.23e-184 AT1G… ARR4
2 2 BraA… 2.64 8.15 678. 1.81e-149 2.16e-145 AT5G… RPL4
3 3 BraA… 2.67 7.37 588. 6.29e-130 5.01e-126 AT1G… ARP1
4 4 BraA… -4.11 7.24 512. 2.09e-113 1.25e-109 AT5G… <NA>
5 5 BraA… 2.58 7.53 497. 3.90e-110 1.86e-106 AT4G… HLN
6 6 BraA… 4.26 7.29 485. 1.51e-107 6.00e-104 AT5G… ATHD2
7 7 BraA… 3.03 5.97 480. 1.91e-106 6.52e-103 AT3G… <NA>
8 8 BraA… 2.50 4.91 478. 6.82e-106 2.04e-102 AT2G… ASHR2
9 9 BraA… 3.16 7.57 475. 2.11e-105 5.60e-102 AT5G… ATHD2
10 10 BraA… 2.25 6.87 460. 5.80e-102 1.39e- 98 AT5G… NAP1;3
# ... with 14,909 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 2 x 12
X1 genes logFC logCPM LR PValue FDR X1_1 AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr> <chr>
1 1 BraA… 2.00 4.58 22.9 1.69e-6 0.0271 23774 AT1G… ARR7
2 2 BraA… 3.95 0.659 22.3 2.27e-6 0.0271 33024 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 2 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.00 4.58 22.9 1.69e-6 0.0271 AT1G… ARR7
2 2 BraA… -3.95 0.659 22.3 2.27e-6 0.0271 AT1G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtdead logFC.densitycr… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.276 -0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… -0.489 -0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… 0.758 2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… 0.189 0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… -0.0786 -1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… 0.192 0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… 0.124 1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… 1.25 -3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… 0.0242 -1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… 0.916 -2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtdead logFC.densityun… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.04 0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… -0.865 0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… 2.90 -2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… 0.903 -0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… -1.30 1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… 0.964 -0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… 1.27 -1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… -2.70 3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… -1.67 1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… -1.09 2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… -0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… -1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… -0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… -1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 370 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.04 7.58 27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
2 2 BraA… -1.30 5.52 24.7 6.80e-7 0.00491 AT2G… <NA>
3 3 BraA… 1.27 4.46 23.8 1.06e-6 0.00491 AT1G… HHO6
4 4 BraA… 0.903 4.94 23.8 1.07e-6 0.00491 AT4G… PDE327
5 5 BraA… 0.964 4.89 23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
6 6 BraA… -1.67 3.11 23.5 1.23e-6 0.00491 AT5G… <NA>
7 7 BraA… 0.856 4.77 22.5 2.13e-6 0.00727 AT4G… ATCAD7
8 8 BraA… 2.90 0.654 21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
9 9 BraA… 0.938 7.04 21.6 3.29e-6 0.00857 AT1G… AtPMT3
10 10 BraA… -0.865 4.13 21.5 3.59e-6 0.00857 AT5G… <NA>
# ... with 360 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtlive logFC.densitycr… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.276 0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… 0.489 0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… -0.758 -2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… -0.189 -0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… 0.0786 1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… -0.192 -0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… -0.124 -1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… -1.25 3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… -0.0242 1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… -0.916 2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 63 x 12
X1 genes logFC.trtlive logFC.densityun… logCPM LR PValue FDR
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.04 -0.766 7.58 29.4 4.09e-7 0.00976
2 2 BraA… 0.865 -0.376 4.13 26.8 1.54e-6 0.0177
3 3 BraA… -2.90 2.15 0.654 25.6 2.74e-6 0.0177
4 4 BraA… -0.903 0.714 4.94 25.2 3.36e-6 0.0177
5 5 BraA… 1.30 -1.22 5.52 24.7 4.23e-6 0.0177
6 6 BraA… -0.964 0.772 4.89 24.6 4.45e-6 0.0177
7 7 BraA… -1.27 1.14 4.46 24.1 5.93e-6 0.0186
8 8 BraA… 2.70 -3.95 0.659 23.9 6.59e-6 0.0186
9 9 BraA… 1.67 -1.70 3.11 23.5 7.77e-6 0.0186
10 10 BraA… 1.09 -2.00 4.58 23.5 7.80e-6 0.0186
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… 0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… 1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.702 4.13 24.5 7.56e-7 0.0181 AT5G… <NA>
2 2 BraA… 0.599 5.50 21.2 4.08e-6 0.0375 AT5G… ORP3C
3 3 BraA… 1.92 0.414 21.0 4.71e-6 0.0375 AT5G… <NA>
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 370 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.04 7.58 27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
2 2 BraA… 1.30 5.52 24.7 6.80e-7 0.00491 AT2G… <NA>
3 3 BraA… -1.27 4.46 23.8 1.06e-6 0.00491 AT1G… HHO6
4 4 BraA… -0.903 4.94 23.8 1.07e-6 0.00491 AT4G… PDE327
5 5 BraA… -0.964 4.89 23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
6 6 BraA… 1.67 3.11 23.5 1.23e-6 0.00491 AT5G… <NA>
7 7 BraA… -0.856 4.77 22.5 2.13e-6 0.00727 AT4G… ATCAD7
8 8 BraA… -2.90 0.654 21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
9 9 BraA… -0.938 7.04 21.6 3.29e-6 0.00857 AT1G… AtPMT3
10 10 BraA… 0.865 4.13 21.5 3.59e-6 0.00857 AT5G… <NA>
# ... with 360 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$leaf.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$leaf.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
# LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
# At_short_description <chr>, perc_ID <dbl>
$root.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 3,887 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.96 4.70 87.7 7.54e-21 1.07e-16 AT1G… ASP4
2 2 BraA… 1.22 5.63 87.6 8.17e-21 1.07e-16 AT2G… <NA>
3 3 BraA… 1.28 5.28 83.6 6.07e-20 5.29e-16 AT1G… BRR2
4 4 BraA… -1.15 5.99 81.6 1.70e-19 1.11e-15 AT2G… <NA>
5 5 BraA… 1.14 7.09 75.2 4.17e-18 2.18e-14 AT1G… BRR2
6 6 BraA… 1.02 5.44 74.1 7.24e-18 3.16e-14 AT5G… <NA>
7 7 BraA… 1.94 3.77 71.4 2.91e-17 1.09e-13 AT3G… TIC
8 8 BraA… 0.928 7.49 69.8 6.47e-17 2.03e-13 AT2G… ATGSL03
9 9 BraA… 1.59 3.73 69.7 6.98e-17 2.03e-13 AT1G… ASU1
10 10 BraA… 1.30 3.72 66.9 2.79e-16 7.10e-13 AT5G… <NA>
# ... with 3,877 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.88 0.498 5.32 778. 1.17e-169
2 2 BraA… 2.50 -0.287 4.42 511. 1.05e-111
3 3 BraA… -3.53 1.22 6.17 491. 2.16e-107
4 4 BraA… -3.95 1.12 4.01 486. 2.51e-106
5 5 BraA… -4.44 -0.0881 4.23 454. 2.05e- 99
6 6 BraA… -2.58 0.467 6.28 445. 2.56e- 97
7 7 BraA… 2.08 -0.172 7.33 441. 2.06e- 96
8 8 BraA… 3.07 0.696 4.36 421. 4.47e- 92
9 9 BraA… -3.22 0.782 5.90 383. 5.42e- 84
10 10 BraA… -2.31 0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densitycr logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -2.38 -0.498 5.32 778. 1.17e-169
2 2 BraA… 2.21 0.287 4.42 511. 1.05e-111
3 3 BraA… -2.31 -1.22 6.17 491. 2.16e-107
4 4 BraA… -2.83 -1.12 4.01 486. 2.51e-106
5 5 BraA… -4.53 0.0881 4.23 454. 2.05e- 99
6 6 BraA… -2.11 -0.467 6.28 445. 2.56e- 97
7 7 BraA… 1.90 0.172 7.33 441. 2.06e- 96
8 8 BraA… 3.76 -0.696 4.36 421. 4.47e- 92
9 9 BraA… -2.44 -0.782 5.90 383. 5.42e- 84
10 10 BraA… -1.62 -0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… 2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… -4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… 1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… -2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… 3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… 6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… -2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… 2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… -3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… 2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… -4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… 1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… -2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… 3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… 6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… -2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… 2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… -3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… 1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… 1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… 3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… 1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… 3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… 3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… 1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… 2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… 1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… -1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… -1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… -3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… -1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… -3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… -3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… -1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… -2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… -1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.88 -0.498 5.32 778. 1.17e-169
2 2 BraA… -2.50 0.287 4.42 511. 1.05e-111
3 3 BraA… 3.53 -1.22 6.17 491. 2.16e-107
4 4 BraA… 3.95 -1.12 4.01 486. 2.51e-106
5 5 BraA… 4.44 0.0881 4.23 454. 2.05e- 99
6 6 BraA… 2.58 -0.467 6.28 445. 2.56e- 97
7 7 BraA… -2.08 0.172 7.33 441. 2.06e- 96
8 8 BraA… -3.07 -0.696 4.36 421. 4.47e- 92
9 9 BraA… 3.22 -0.782 5.90 383. 5.42e- 84
10 10 BraA… 2.31 -0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 8,708 x 12
X1 genes logFC.densityun logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 2.38 0.498 5.32 778. 1.17e-169
2 2 BraA… -2.21 -0.287 4.42 511. 1.05e-111
3 3 BraA… 2.31 1.22 6.17 491. 2.16e-107
4 4 BraA… 2.83 1.12 4.01 486. 2.51e-106
5 5 BraA… 4.53 -0.0881 4.23 454. 2.05e- 99
6 6 BraA… 2.11 0.467 6.28 445. 2.56e- 97
7 7 BraA… -1.90 -0.172 7.33 441. 2.06e- 96
8 8 BraA… -3.76 0.696 4.36 421. 4.47e- 92
9 9 BraA… 2.44 0.782 5.90 383. 5.42e- 84
10 10 BraA… 1.62 0.691 4.98 375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… -2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… 4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… -1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… 2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… -3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… -6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… 2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… -2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… 3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 8,363 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.62 5.32 656. 1.22e-144 3.21e-140 AT1G… AST56
2 2 BraA… -2.36 4.42 494. 1.97e-109 2.60e-105 AT1G… NLP4
3 3 BraA… 4.48 4.23 458. 1.38e-101 1.22e- 97 AT3G… ATIPT3
4 4 BraA… -1.99 7.33 436. 9.96e- 97 6.56e- 93 AT5G… AAP2
5 5 BraA… 2.34 6.28 395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB
6 6 BraA… -3.38 4.35 370. 2.32e- 82 1.02e- 78 AT5G… <NA>
7 7 BraA… -6.68 3.06 368. 5.13e- 82 1.93e- 78 AT3G… NLP9
8 8 BraA… 2.47 5.28 358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
9 9 BraA… -2.81 4.13 342. 1.82e- 76 5.33e- 73 AT5G… <NA>
10 10 BraA… 3.34 4.01 336. 4.16e- 75 1.04e- 71 AT5G… <NA>
# ... with 8,353 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 471 x 12
X1 genes logFC logCPM LR PValue FDR X1_1 AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr> <chr>
1 1 BraA… -2.06 4.03 41.3 1.28e-10 3.36e-6 15390 AT3G… BHLH039
2 2 BraA… -1.60 5.88 36.8 1.33e- 9 1.75e-5 35547 AT1G… ASP4
3 3 BraA… -1.11 6.78 32.4 1.27e- 8 1.12e-4 23863 AT1G… ATSBT5.2
4 4 BraA… -3.40 5.12 28.1 1.13e- 7 7.45e-4 4032 AT3G… <NA>
5 5 BraA… -1.50 4.22 26.7 2.33e- 7 1.14e-3 1149 AT4G… ATIRT1
6 6 BraA… -3.19 2.39 26.5 2.60e- 7 1.14e-3 39482 AT1G… GAT
7 7 BraA… -3.72 0.831 24.9 6.10e- 7 2.10e-3 28198 AT5G… <NA>
8 8 BraA… -1.72 5.26 24.8 6.39e- 7 2.10e-3 14171 AT5G… AtCOMT
9 9 BraA… -2.14 5.04 24.0 9.43e- 7 2.76e-3 21279 AT3G… F6'H1
10 10 BraA… -1.84 4.05 23.8 1.08e- 6 2.84e-3 771 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 471 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.06 4.03 41.3 1.28e-10 3.36e-6 AT3G… BHLH039
2 2 BraA… 1.60 5.88 36.8 1.33e- 9 1.75e-5 AT1G… ASP4
3 3 BraA… 1.11 6.78 32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2
4 4 BraA… 3.40 5.12 28.1 1.13e- 7 7.45e-4 AT3G… <NA>
5 5 BraA… 1.50 4.22 26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1
6 6 BraA… 3.19 2.39 26.5 2.60e- 7 1.14e-3 AT1G… GAT
7 7 BraA… 3.72 0.831 24.9 6.10e- 7 2.10e-3 AT5G… <NA>
8 8 BraA… 1.72 5.26 24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT
9 9 BraA… 2.14 5.04 24.0 9.43e- 7 2.76e-3 AT3G… F6'H1
10 10 BraA… 1.84 4.05 23.8 1.08e- 6 2.84e-3 AT4G… <NA>
# ... with 461 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtdead logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 0.370 1.60 5.88 105. 1.40e-23
2 2 BraA… 0.0552 2.06 4.03 77.8 1.27e-17
3 3 BraA… 0.372 0.682 6.91 73.4 1.16e-16
4 4 BraA… 0.211 1.50 4.22 65.5 5.99e-15
5 5 BraA… -0.523 -0.132 8.54 63.6 1.56e-14
6 6 BraA… -0.331 -0.590 7.24 60.6 6.97e-14
7 7 BraA… -2.20 1.84 2.44 59.1 1.50e-13
8 8 BraA… -2.52 1.41 1.76 58.1 2.36e-13
9 9 BraA… -0.128 -0.895 5.25 56.8 4.62e-13
10 10 BraA… -0.231 -0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtdead logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… 1.97 -1.60 5.88 105. 1.40e-23
2 2 BraA… 2.11 -2.06 4.03 77.8 1.27e-17
3 3 BraA… 1.05 -0.682 6.91 73.4 1.16e-16
4 4 BraA… 1.71 -1.50 4.22 65.5 5.99e-15
5 5 BraA… -0.655 0.132 8.54 63.6 1.56e-14
6 6 BraA… -0.921 0.590 7.24 60.6 6.97e-14
7 7 BraA… -0.353 -1.84 2.44 59.1 1.50e-13
8 8 BraA… -1.12 -1.41 1.76 58.1 2.36e-13
9 9 BraA… -1.02 0.895 5.25 56.8 4.62e-13
10 10 BraA… -1.22 0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… 2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… 1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… 0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… -1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… 0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… -0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… -0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… 0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… -0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… 2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… 1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… 0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… -1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… 0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… -0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… -0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… 0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… -0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,434 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 1.97 5.88 101. 9.26e-24 2.44e-19 AT1G… ASP4
2 2 BraA… 2.11 4.03 77.7 1.18e-18 1.55e-14 AT3G… BHLH039
3 3 BraA… 1.05 6.91 65.1 7.00e-16 6.15e-12 AT1G… ATOPR2
4 4 BraA… 1.71 4.22 64.3 1.05e-15 6.92e-12 AT4G… ATIRT1
5 5 BraA… -1.02 5.25 55.9 7.52e-14 3.96e-10 AT5G… <NA>
6 6 BraA… -0.921 7.24 53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03
7 7 BraA… -1.22 5.48 53.3 2.83e-13 1.07e- 9 AT2G… <NA>
8 8 BraA… 1.81 5.26 51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT
9 9 BraA… 1.16 5.96 50.9 9.52e-13 2.30e- 9 AT2G… <NA>
10 10 BraA… -1.24 3.91 50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F
# ... with 3,424 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 357 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -2.20 2.44 57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12
2 2 BraA… -2.52 1.76 47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59
3 3 BraA… -4.03 0.831 46.6 8.91e-12 7.82e- 8 AT5G… <NA>
4 4 BraA… -1.40 3.53 41.0 1.52e-10 1.00e- 6 AT1G… HMS
5 5 BraA… -1.35 2.35 38.1 6.87e-10 3.27e- 6 AT2G… ANAC042
6 6 BraA… -2.08 3.27 37.9 7.45e-10 3.27e- 6 AT2G… <NA>
7 7 BraA… -1.97 5.83 34.1 5.13e- 9 1.93e- 5 AT4G… <NA>
8 8 BraA… -0.925 4.26 32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1
9 9 BraA… -1.86 2.87 32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042
10 10 BraA… -1.90 1.61 31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2
# ... with 347 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtlive logFC.densitycr… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -0.370 -1.60 5.88 105. 1.40e-23
2 2 BraA… -0.0552 -2.06 4.03 77.8 1.27e-17
3 3 BraA… -0.372 -0.682 6.91 73.4 1.16e-16
4 4 BraA… -0.211 -1.50 4.22 65.5 5.99e-15
5 5 BraA… 0.523 0.132 8.54 63.6 1.56e-14
6 6 BraA… 0.331 0.590 7.24 60.6 6.97e-14
7 7 BraA… 2.20 -1.84 2.44 59.1 1.50e-13
8 8 BraA… 2.52 -1.41 1.76 58.1 2.36e-13
9 9 BraA… 0.128 0.895 5.25 56.8 4.62e-13
10 10 BraA… 0.231 0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,857 x 12
X1 genes logFC.trtlive logFC.densityun… logCPM LR PValue
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 BraA… -1.97 1.60 5.88 105. 1.40e-23
2 2 BraA… -2.11 2.06 4.03 77.8 1.27e-17
3 3 BraA… -1.05 0.682 6.91 73.4 1.16e-16
4 4 BraA… -1.71 1.50 4.22 65.5 5.99e-15
5 5 BraA… 0.655 -0.132 8.54 63.6 1.56e-14
6 6 BraA… 0.921 -0.590 7.24 60.6 6.97e-14
7 7 BraA… 0.353 1.84 2.44 59.1 1.50e-13
8 8 BraA… 1.12 1.41 1.76 58.1 2.36e-13
9 9 BraA… 1.02 -0.895 5.25 56.8 4.62e-13
10 10 BraA… 1.22 -0.989 5.48 55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
# At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… -2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… -1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… -0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… 1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… -0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… 0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… 0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… -0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… 0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3,352 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 0.590 8.54 62.3 2.94e-15 7.74e-11 AT2G… ATUBC24
2 2 BraA… -2.18 1.59 55.7 8.55e-14 1.13e- 9 AT2G… <NA>
3 3 BraA… -1.10 2.65 49.2 2.27e-12 1.99e- 8 AT1G… <NA>
4 4 BraA… -0.482 6.84 46.0 1.17e-11 7.35e- 8 AT4G… <NA>
5 5 BraA… 1.61 1.61 45.3 1.67e-11 7.35e- 8 AT1G… IGMT2
6 6 BraA… -0.607 5.95 45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4
7 7 BraA… 0.528 6.88 44.9 2.07e-11 7.35e- 8 AT1G… ABCG35
8 8 BraA… 0.499 7.51 44.8 2.23e-11 7.35e- 8 AT1G… FB
9 9 BraA… -0.714 6.91 44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2
10 10 BraA… 0.569 6.15 43.5 4.27e-11 1.13e- 7 AT5G… CLPD
# ... with 3,342 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,434 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… -1.97 5.88 101. 9.26e-24 2.44e-19 AT1G… ASP4
2 2 BraA… -2.11 4.03 77.7 1.18e-18 1.55e-14 AT3G… BHLH039
3 3 BraA… -1.05 6.91 65.1 7.00e-16 6.15e-12 AT1G… ATOPR2
4 4 BraA… -1.71 4.22 64.3 1.05e-15 6.92e-12 AT4G… ATIRT1
5 5 BraA… 1.02 5.25 55.9 7.52e-14 3.96e-10 AT5G… <NA>
6 6 BraA… 0.921 7.24 53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03
7 7 BraA… 1.22 5.48 53.3 2.83e-13 1.07e- 9 AT2G… <NA>
8 8 BraA… -1.81 5.26 51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT
9 9 BraA… -1.16 5.96 50.9 9.52e-13 2.30e- 9 AT2G… <NA>
10 10 BraA… 1.24 3.91 50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F
# ... with 3,424 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 357 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.20 2.44 57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12
2 2 BraA… 2.52 1.76 47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59
3 3 BraA… 4.03 0.831 46.6 8.91e-12 7.82e- 8 AT5G… <NA>
4 4 BraA… 1.40 3.53 41.0 1.52e-10 1.00e- 6 AT1G… HMS
5 5 BraA… 1.35 2.35 38.1 6.87e-10 3.27e- 6 AT2G… ANAC042
6 6 BraA… 2.08 3.27 37.9 7.45e-10 3.27e- 6 AT2G… <NA>
7 7 BraA… 1.97 5.83 34.1 5.13e- 9 1.93e- 5 AT4G… <NA>
8 8 BraA… 0.925 4.26 32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1
9 9 BraA… 1.86 2.87 32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042
10 10 BraA… 1.90 1.61 31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2
# ... with 347 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
$root.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 297 x 11
X1 genes logFC logCPM LR PValue FDR AGI At_symbol
<int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
1 1 BraA… 2.19 2.37 56.7 5.00e-14 1.30e-9 AT1G… ATGSTU12
2 2 BraA… 2.06 3.30 47.4 5.87e-12 5.83e-8 AT2G… <NA>
3 3 BraA… 4.05 0.567 47.1 6.75e-12 5.83e-8 AT5G… <NA>
4 4 BraA… 2.52 1.68 46.1 1.13e-11 7.29e-8 AT2G… ATWRKY59
5 5 BraA… -2.17 1.80 45.7 1.41e-11 7.32e-8 AT2G… <NA>
6 6 BraA… 1.41 2.87 43.4 4.55e-11 1.97e-7 AT1G… HMS
7 7 BraA… 1.86 2.20 38.3 5.95e-10 2.20e-6 AT2G… ANAC042
8 8 BraA… 0.933 4.20 38.0 7.03e-10 2.28e-6 AT4G… CYP706A1
9 9 BraA… 1.46 1.59 37.5 9.38e-10 2.70e-6 AT5G… <NA>
10 10 BraA… 1.90 1.67 36.6 1.48e- 9 3.84e-6 AT1G… IGMT2
# ... with 287 more rows, and 2 more variables:
# At_short_description <chr>, perc_ID <dbl>
DEG.count.list.e3.v3.0annotation.all.FDR0.05[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% View() # OK. 3887 genes
